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Enhanced malic acid production from glycerol with high-cell density Ustilago trichophora TZ1 cultivations



In order to establish a cost-efficient biodiesel biorefinery, valorization of its main by-product, crude glycerol, is imperative. Recently, Ustilago trichophora TZ1 was found to efficiently produce malic acid from glycerol. By adaptive laboratory evolution and medium optimization, titer and rate could be improved significantly.


Here we report on the investigation of this strain in fed-batch bioreactors. With pH controlled at 6.5 (automatic NaOH addition), a titer of 142 ± 1 g L−1 produced at an overall rate of 0.54 ± 0.00 g L−1 h−1 was reached by optimizing the initial concentrations of ammonium and glycerol. Combining the potential of bioreactors and CaCO3 as buffer system, we were able to increase the overall production rate to 0.74 ± 0.06 g L−1 h−1 with a maximum production rate of 1.94 ± 0.32 g L−1 reaching a titer of 195 ± 15 g L−1. The initial purification strategy resulted in 90 % pure calcium malate as solid component. Notably, the fermentation is not influenced by an increased temperature of up to 37 °C, which reduces the energy required for cooling. However, direct acid production is not favored as at a lowered pH value of pH 4.5 the malic acid titer decreased to only 9 ± 1 g L−1. When using crude glycerol as substrate, only the product to substrate yield is decreased. The results are discussed in the context of valorizing glycerol with Ustilaginaceae.


Combining these results reveals the potential of U. trichophora TZ1 to become an industrially applicable production host for malic acid from biodiesel-derived glycerol, thus making the overall biodiesel production process economically and ecologically more feasible.


The production of biodiesel, as one possible supplement for petroleum-derived fuels, is a great opportunity to drive the needed switch to a bio-based economy. This is also reflected in the ever increasing amount of produced biodiesel, which is predicted to be 123 million tons per year for 2016 [1]. However, this process results in a 10 % (w/v) waste stream of crude glycerol, decreasing the profit margin and the ecological feasibility. Valorization of this large low-value side stream by microbial conversion is considered as a promising strategy to add value to the overall biodiesel biorefinery concept. Microbial production processes starting from glycerol as substrate have been investigated and reviewed intensively over the last years resulting in production processes for many different products [24].

The C4-dicarboxylic acid malic acid is widely used as acidulant and flavor enhancer in the food industry and has also received great interest in non-food applications, such as metal cleaning, textile finishing, and pharmaceuticals production [5]. Even though the annual world production in 2006 was only about 40,000 tons, future use of malic acid is predicted to be above 200,000 tons per year as raw material of a novel biodegradable polymer–polymalic acid [5, 6]. In 2004, malic acid has been identified by the Department of Energy (DOE) as one of the top twelve building block chemicals to be produced from renewable biomass at bulk scale [7]. Traditionally, malic acid was obtained by the extraction from apple juice at low yields [8]. Today malic acid can be produced both chemically and biotechnologically. In current industrial production processes, it is mainly manufactured by chemical synthesis via hydration of maleic or fumaric acid producing a racemic mixture of d- and l-isomers [9]. Alternatively, enzymatic hydration of fumarate by immobilized bacterial cells of Brevibacterium ammoniagenes or Bacillus flavum containing a highly active fumarase yields enantiomerically pure l-malic acid [10]. However, these production methods are costly and substrates for the synthesis of malic acid are derived from non-sustainable petrochemical feedstocks [5]. Thus, as TCA cycle intermediate, bio-based microbiological production processes based on renewable substrates for malic acid have become the focus of research. The first patented microorganism producing malic acid was Aspergillus flavus [11]. The fermentation process was improved by medium optimization resulting in a final titer of 113 from 120 g L−1 glucose as substrate [8]. However, this organism is not applicable for industrial malic acid production, especially for food applications, due to the production of aflatoxins [12]. Besides Escherichia coli [13, 14] and Saccharomyces cerevisiae [15], an Aspergillus oryzae strain has been investigated as production organism. This strain, overexpressing a C4-dicarboxylate transporter, pyruvate carboxylase, and malate dehydrogenase produced a final titer of 154 g L−1 malic acid from glucose at a rate of 0.94 g L−1 h−1 [16].

Recently we reported that Ustilago trichophora TZ1, a member of the family of Ustilaginaceae which is known to produce organic acids naturally [17], is able to produce malic acid from glycerol [18]. This strain has been adapted to glycerol by laboratory evolution, increasing glycerol uptake rates. After medium optimization, the final malic acid titer reached 196 g L−1 produced from 250 g L−1 glycerol at an average rate of 0.4 g L−1 h−1 in shake flasks. The limiting factor in these shake flask cultivations was either glycerol depletion or problems concerning oxygen transfer, which result from viscous culture broth.

Here we report on malic acid production with U. trichophora TZ1 in bioreactors to overcome abovementioned problems. Further, the production process was investigated at differing temperature profiles and pH values to determine the boundary conditions of an eventual industrial process, and the effects of using high concentrations of crude glycerol as a substrate were evaluated.

Results and discussion

Bioreactors enable higher cell density resulting in higher volumetric production rates

The potential of Ustilaginaceae as production organisms of different industrially relevant compounds, such as organic acids, lipids, or polyols, has been discussed and demonstrated consistently over the last years [17, 1925]. Recently, U. trichophora was found to produce malic acid naturally from glycerol at high titers. By adaptive laboratory evolution and medium optimization, the production rate of this strain in shake flask could be improved to around 0.4 g L−1 h−1 reaching titers near 200 g L−1 [18]. All cultivations ended either upon glycerol depletion or by oxygen limitations due to the viscosity of the cultures. These viscosity issues resulted mainly from the buffering agent, CaCO3, reacting with produced malate, forming insoluble calcium malate. Although this precipitation might be beneficial for alleviation of product inhibition, it greatly hinders oxygenation of the culture broth in shaking flasks [26].

To overcome handling issues with insoluble components and to avoid glycerol depletion, here we investigate the production process with U. trichophora TZ1 in bioreactors, in which the pH was kept constant by titration with NaOH. By this, effects of insoluble buffer components on production can be minimized. Further, by feeding additional glycerol prior to depletion, malate titers might be further increased. Additionally, better oxygenation through sparging and stirring, which has a strong influence on microbial organic acid production processes [27], also enables higher cell densities.

Initially, U. trichophora TZ1 was cultured in pH controlled bioreactors (pH 6.5, NaOH titration) in MTM containing 0.8 g L−1 NH4Cl and 200 g L−1 initial glycerol. An additional 160 g glycerol was fed when the concentration dropped below 50 g L−1. This results in a slight drop in the measured malate concentrations due to the dilution of the culture broth. The resulting titer (119.9 ± 0.9 g L−1) and rate (0.13 ± 0.00 g L−1 h−1) (Fig. 1b) were significantly lower than those reached in shake flasks with CaCO3 [18]. Likely, these reductions can be attributed to product inhibition caused by the drastically increased dissolved malate concentration in NaOH-titrated cultures. To improve the production rate, the cell density was increased by using higher concentrations of the growth-limiting nutrient NH4Cl (1.6, 3.2, and 6.4 g L−1). Dependent on the initial NH4Cl concentration, a delay in the onset of malate production could be observed, which can be attributed to a longer growth phase. Maximal OD600, however, could be increased from 42 ± 2 with 0.8 g L−1 NH4Cl to 80 ± 0 and 115 ± 1 using 1.6 and 3.2 g L−1 NH4Cl, respectively (Fig. 1a). As expected, also the overall volumetric malic acid production rate (from the beginning of cultivation until the end) increased to 0.46 ± 0.02 and 0.54 ± 0.07 g L−1 h−1 with 1.6 and 3.2 g L−1 NH4Cl, respectively (Fig. 1b). 6.4 g L−1 NH4Cl, however, did not lead to increased biomass and subsequently production, but had the opposite effect (data not shown). In these cultures, NH4Cl was no longer depleted during the fermentation. A similar effect was observed for itaconate producing Ustilago maydis MB215 in MTM with NH4Cl concentrations above 4 g L−1 [19]. This likely explains the reduced productivity, since nitrogen limitation is the most efficient trigger for organic acid production with Ustilaginaceae [28]. To compensate for this effect, all medium components except for glycerol were doubled in combination with 6.4 g L−1 NH4Cl in a subsequent fermentation, resulting in an overall volumetric production rate of 0.54 ± 0.00 g L−1 h−1, with a maximal production rate of 1.99 ± 0.04 g L−1 h−1 between 45 and 69 h (Fig. 1b).

Fig. 1
figure 1

Fermentation of Ustilago trichophora TZ1 with different NH4Cl concentrations. a OD600, b malate production, c maximum malate production rate (solid bars) and yield (open bars) for controlled batch fermentations in MTM containing 200 g L−1 initial glycerol at 30 °C and pH 6.5 with DO kept at 80 %. Colors indicate different initial NH4Cl concentrations: 0.8 g L−1 (circles, blue), 1.6 g L−1 (diamonds, green), 3.2 g L−1 (squares, red), and 6.4 g L−1 with doubled concentrations of all medium components except glycerol (triangles, black). Values for 0.8 g L−1 are only shown until 432 h; however, a further increase in concentration to a final titer of 120 ± 1 g L−1 could be observed until 908 h of cultivation. Error bars indicate deviation from the mean (n = 2)

As expected, an increase in the growth-limiting nutrient led to more biomass formation and consequently to a higher volumetric production rate. There is a good correlation between the maximum malate production rate and the initial NH4Cl concentration, indicating that the production rate could be further increased as long as secondary limitations are excluded. However, further increases will strongly impact the product yield, since more glycerol is used for biomass formation. Assuming no CO2 co-consumption, the maximum theoretical yield would be 0.75 mol malate per mole glycerol. However, the glycerol needed for biomass production reduces this maximum, and this reduction is proportional to the initial ammonium concentration. Based on the glycerol consumption during the growth phase (Fig. 1a), approximately 11.5 g of glycerol are needed for biomass formation per gram NH4Cl. Thus, taking into account the total amount of glycerol consumed by each culture, biomass formation reduces the maximum theoretical yield to 0.73, 0.71, 0.68, and 0.62 mol mol−1, for 0.8, 1.6, 3.2, and 6.4 g L−1 NH4Cl, respectively. This in part explains the reduction in the observed yields in the cultures with higher NH4Cl concentrations, although in general the yields are only 30–55 % of these theoretical maxima, suggesting that the impact of biomass formation is at the moment relatively low. Improvement in the product yield should be the main focus of future optimization, possibly by the reduction in by-product formation through the disruption of competing pathways. The improvement in specificity for the production of one organic acid is generally considered a promising approach to improve microbial organic acid production. For U. trichophora TZ1, however, besides 5–10 g L−1 succinate, no significant amounts of other organic acids were found in HPLC analysis. Additionally, CO2 and extra- and intracellular lipids are most likely the main by-products. The formation of lipids under organic acid production conditions and their effect on the cells have been described extensively [28, 29]. These by-products can be reduced by knock-out of single genes in the responsive gene clusters [3032].

Since a significant influence of the starting glycerol concentration on the malic acid production rate has been observed in shake flasks [18], this relation was also studied in bioreactors. Concentration steps of 50 g L−1 between 150 and 300 g L−1 were investigated in MTM containing 3.2 g L−1 NH4Cl. Additional 160 g glycerol was fed to the cultures one time (300 g L−1 initial glycerol), two times (150 and 200 g L−1 initial glycerol), and four times (250 g L−1 initial glycerol), when the concentration became lower than 50–100 g L−1 (150 and 200 g L−1 initial glycerol) or 200 g L−1 (250 and 300 g L−1 initial glycerol). Thus, after the consumption of the initial glycerol, its concentrations generally ranged between 50 and 150 g L−1 (150 and 200 g L−1 initial glycerol) and 100 and 250 g L−1 (250 and 300 g L−1 initial glycerol). Just as in shake flasks, increasing initial glycerol concentrations between 150 and 300 g L−1 decreased growth rates, final OD600 and malic acid production rates (Fig. 2). Possibly, higher glycerol concentrations impose a stress upon the cells. This is also known in other organisms, such as S. cerevisiae, even though lower glycerol concentrations are generally known to contribute to osmotolerance in different yeast, such as Zygosaccharomyces rouxii and S. cerevisiae [33, 34].

Fig. 2
figure 2

Fermentation of Ustilago trichophora TZ1 with different initial glycerol concentrations. a OD600, b malate production for fermentations in MTM containing 3.2 g L−1 NH4Cl at 30 °C and pH 6.5 with DO kept at 80 %. Colors indicate different initial glycerol concentrations: 300 g L−1 (circles, blue), 250 g L−1 (diamonds, green), 200 g L−1 (squares, red), 150 g L−1 (triangles, black). Additional 160 g glycerol was added when the concentration dropped below 50 g L−1. Error bars indicate deviation from the mean (n = 2)

Ustilago trichophora TZ1 accepts a broad temperature range for production

In 1990, Guevarra and Tabuchi investigated the influence of temperature on itaconic acid production and growth of Ustilago cynodontis [35]. They could show that the highest tested temperature (35 °C) was best for cell growth. However, the lowest tested temperature (25 °C) resulted in the highest organic acid titers. To investigate influences of temperature on acid production by U. trichophora TZ1, cells were grown at 30 °C and the temperature was changed after the growth phase to 25 and 35 °C. In a third approach, heating was disabled and cooling was only activated at temperatures exceeding 37 °C (Fig. 3). In this case, the temperature remained at this maximum after 30 h, indicating the considerable heat generated by these high-density cultures. As shown in Fig. 3b, malic acid production was not influenced by temperatures exceeding 30 °C. However, 25 °C resulted in a lower malic acid production rate yet reaching the same final titer of approximately 120 g L−1.

Fig. 3
figure 3

Fermentation of Ustilago trichophora TZ1 at different temperatures. a OD600, b malate concentration for fermentations in MTM containing 200 g L−1 initial glycerol and 3.2 g L−1 NH4Cl at 30 °C and pH 6.5 with DO kept at 80 %. Colors indicate different temperatures: 25 °C (triangles, black), 30 °C (squares, red), 35 °C (circles, blue), and 37 °C (diamonds, green). Error bars indicate deviation from the mean (n = 2)

Since malic acid production with U. trichophora TZ1 was not influenced by elevated temperatures and reduced use of heating and cooling systems could reduce operating costs, preliminary experiments without a heating and cooling system were conducted. These experiments indicated that uncontrolled temperatures above 37 °C negatively influence the malic acid production process. This was also observed in 2008 by Kuenz for itaconic acid production with Aspergillus terreus [36]. A temperature increase from 27 to 30 °C resulted in a 60 % increased production rate. Further increasing the temperature to 33 and 37 °C resulted in a 20–40 % increase compared to 30 °C. However, a process temperature of 40 °C reduced itaconic acid production drastically [36].

Decreasing pH values drastically lower malic acid production

In a next step, the fermentation was investigated in respect to growth medium pH. Malic acid production with U. trichophora TZ1 was investigated in bioreactors at pH 4.5, 5.5, and 6.5. The tested pH range neither influenced growth rate (Fig. 4a), nor morphology (data not shown). However, maximal OD600 was higher at lower pH. Malic acid production was clearly lowered by decreasing pH reaching 113 ± 15 g L−1 (pH 6.5), 64 ± 6 g L−1 (pH 5.5), and 9 ± 1 g L−1 (pH 4.5). In fungi such as Aspergillus, Saccharomyces, and Yarrowia, organic acids such as succinate, itaconate, and malate are produced best at low pH, with some exceptions [27, 3741]. For Ustilaginaceae, mainly near neutral pH values are best for organic acid production [19], although exceptions such as U. cynodontis have been reported [17].

Fig. 4
figure 4

Fermentation of Ustilago trichophora TZ1 at different pH values. a OD600, b malate concentration for fermentations in MTM containing 200 g L−1 initial glycerol and 3.2 g L−1 NH4Cl at 30 °C and pH 6.5 with DO kept at 80 %. Additional 160 g glycerol was added when the concentration dropped below 50 g L−1. Colors indicate different pH values: pH 6.5 (red), 5.5 (blue), and 4.5 (green). Error bars indicate deviation from the mean (n = 2). c Distribution of molar fractions of dissociated and (partly) undissociated malate species. Shown is the relative distribution of fully dissociated (blue), partially dissociated (black) and fully undissociated (red) malate dependent on the pH value. Data were generated using CurTiPot [56]

Production both at high and at low pH value has different opportunities and disadvantages on microbial organic acid production and downstream processing. A low pH can help to lower the risk of contamination in industrial-scale fermentations. Further, the production of environmentally unfriendly by-products can be reduced, since during the production process less titration agents, such as CaCO3 or Ca(OH)2, are needed, which in the later process have to be disposed of. However, the same by-product, namely gypsum, is also produced in the downstream process of microbial citric acid production, resulting from the reaction of sulfuric acid with calcium–citrate [42]. However, more advanced downstream technologies, such as simulated moving bed [43], are becoming ever more established and could enable a calcium-free process, provided that it does not negatively impact the overall process efficiency. Another advantage of producing acids at low pH is the easier downstream processing itself, since methods such as cooling, evaporation–crystallization or salting [20, 44] are possible. Besides the positive effects of production at a low pH, there are many advantages for production at near neutral pH. One of those beneficial effects for Ustilaginaceae is the lowered burden, normally resulting from undissociated acids or low pH itself. Other advantages are the avoidance of thermodynamic constraints on acid export or the possibility of advanced process strategies, such as simultaneous saccharification and fermentation (SSF) in which the pH optimum of the applied enzymes is essential [6, 28, 45].

pH values near the lower pKa value of malate (pKa1 3.46, pKa2 5.10) [15] result in undissociated malic acid. Although the molar fraction of this undissociated species is relatively low (approximately 0.002 % at pH 6.5, 0.1 % at pH 5.5 and 4.8 % at pH 4.5; Fig. 4c), its protonophoric effect likely disrupts cellular pH homeostasis. This, possibly coupled to an increased intracellular malic acid concentration, likely leads to the observed reduction in malate production. The weak acid uncoupling effect caused by uptake of the protonated form via diffusion with a simultaneous import of a proton and needed active transport of the dissociated form out of the cell leads to a loss of energy [45, 46]. A further loss of energy can result from the export mechanism itself. It was reported that the most likely mechanism for export of dicarboxylic acids at low pH is an antiport with protons [47]. This would lead to additional H+ ions pumped against the proton motive force, which consequently increases ATP consumption [48]. The observation that glycerol uptake is not decreased in cultures with lower pH, would strengthen this hypothesis, since its consumption could help to cope with the energy loss.

CaCO3 as buffering agent helps to overcome product inhibition

Independent from final OD600, malic acid production, glycerol consumption, growth rate, and temperature, a clear drop in production rate at malate concentrations above 100 g L−1 is visible and the maximal titer of around 140 g L−1 was not exceeded. In shake flask cultivations containing CaCO3 as buffer agent, however, this titer had been exceeded with constant production rates until glycerol depletion [18]. In these cultures, the CaCO3 reacts with the produced malic acid forming calcium malate, which precipitates at a concentration above 14 g L−1. As a consequence, additionally produced malate is no longer dissolved in the medium, thus alleviating product inhibition and toxicity. These results strongly suggest a negative effect of product inhibition at concentrations above 100 g L−1.

To overcome the assumed product inhibition in fed-batch bioreactors, cultivations with MTM containing 3.2 g L−1 NH4Cl, 200 g L−1 initial glycerol and 100 g L−1 CaCO3 as buffer were performed (Fig. 5). An additional 150 g L−1 CaCO3 was added when the pH dropped below 5.5 and additional 160 g glycerol was fed when the concentration fell below 50 g L−1. This fermentation resulted in the production of 195 ± 15 g L−1 of malic acid within 264 h of cultivation, corresponding to an overall production rate of 0.74 ± 0.06 g L−1 h−1. The process reached a yield of 0.43 ± 0.05 gmal g −1gly and a maximal production rate of 1.94 ± 0.32 g L−1 between 47 and 71 h (Fig. 5a). Both glycerol consumption and malic acid production decreased over time. The yield during production phase, however, stayed constant in a range of 0.39–0.49 gmal g −1gly , indicating that the decreasing production rate is rather an effect of dilution due to glycerol feed than an actual decrease in the specific productivity.

Fig. 5
figure 5

Fermentation of Ustilago trichophora TZ1 with CaCO3. a malate concentration (squares) and glycerol concentration (circles), b fermentation broth after 264 h of fermentation in MTM containing 200 g L−1 glycerol, 3.2 g L−1 NH4Cl and 100 g L−1 initial CaCO3 at 30 °C with DO kept at 80 %

The yield achieved with CaCO3 as buffer is 1.5-fold higher than with NaOH. This increase may either be due to an increase in CO2 co-fixation through the action of pyruvate carboxylase or to a reduction in product inhibition by in situ crystallization of calcium malate. Based on the current yield, and assuming that all remaining glycerol is converted to CO2, 85 % of the total produced CO2 originates from glycerol. The remaining 15 % originates from CaCO3 (12 %) and aeration (3 %). Given this relatively low contribution of CaCO3 to the overall CO2 balance, a positive effect of additional CO2 co-metabolism from CaCO3 is unlikely. This suggests that the higher yield observed with CaCO3 is mainly due to reduction in product inhibition.

At 264 h, the fermentation had to be stopped due to bad mixing caused by high medium viscosity (Fig. 5b) as had already been experienced for shake flask cultivations using CaCO3 as buffering agent [18]. This increased viscosity, likely caused by calcium malate, results in poor and inhomogeneous oxygenation. Further, even though the formed calcium malate can easily be recovered for downstream processing, it is linked to a large stream of gypsum waste, which results from the reaction with sulfuric acid within the downstream process as already mentioned above [42]. This gypsum needs to be disposed of as environmentally unfriendly leftover of this process. However, the prior limit of 140 g L−1 malic acid in bioreactors could be exceeded, further sustaining the hypothesis of product inhibition at concentrations above 140 g L−1. Additionally, the malic acid production rate could be kept near constant for a longer time. These advantages have to be weighed against the abovementioned drawbacks in order to determine the beneficial effect of CaCO3 as buffering agent.

As already mentioned, the formation of solid calcium malate in bioreactors containing CaCO3 as buffering agent enables efficient initial purification. To isolate the product from the fermentations, all solid components (settled for 48 h) resulting from an autoclaved fermentation with CaCO3 (Fig. 5b) were dried at 120 °C for 24 h. 0.2 g of this mixture was dissolved in 1 mL of HCl (37 %) and adjusted to 2 mL with water in triplicates. The mixture was filtered to remove cells and the malate concentration was determined via HPLC to be 68.1 ± 0.1 g L−1. Assuming that all products are recovered in the form of calcium malate, this is nearly 90 % of the theoretical malic acid concentration (78 g L−1), indicating that the solids recovered from the bioreactor are 90 % pure calcium malate. The remaining 10 % can be assumed to be biomass and remaining CaCO3.

Ustilago trichophora TZ1 can cope with impurities in crude glycerol

Biodiesel-derived crude glycerol contains, depending on the biodiesel production process, impurities such as methanol, ash, soap, salts, non-glycerol organic matter, and water [2, 4]. Even though different microbial conversions of crude glycerol to value-added chemicals have been reported [49], many organisms struggle with the contained impurities, especially in fed-batch cultures with high substrate loads. The purification to pharma-grade glycerol, however, is a costly process often prohibiting the possible application of glycerol in microbial chemical production. To test whether U. trichophora TZ1 is able to cope with the contained impurities, we investigated malic acid production with U. trichophora TZ1 in MTM containing 100 and 200 g L−1 crude glycerol in shake flasks. The used crude glycerol contained 1.5 % ashes and 1.9 % free fatty acids, with a pH value between 6 and 8. Neither growth rate, nor maximal optical density, nor glycerol uptake was influenced by 100 and 200 g L−1 crude glycerol compared to the same amount of pharma-grade glycerol. Malic acid production, however, was lowered by 63 % (100 g L−1) and 41 % (200 g L−1) (data not shown). This indicates that the organism itself is capable of coping with the contained impurities, although at a cost resulting in a lower malic acid titer. This in shake flasks may be due to lower oxygen input as a result of increased salt concentrations, which can be up to 12 % in crude glycerol [4]. Increased osmotic pressure in media containing high concentrations of salts results in a lower maximum oxygen transfer rate in shake flasks [50]. The effect of this on growth and organic acid production was investigated in several organisms. For U. maydis, increased osmotic stress due to higher salt concentrations resulted in a prolonged lag-phase and lower growth rates. Interestingly, itaconic acid production slightly increased with higher salt concentrations [28], possibly due to high redox energy surplus generated with this product compared to malate. The same effect was observed in Candida oleophila with increased citric acid production with higher osmolarity of the medium [51]. Since the redox potential of the different production pathways for malic acid, succinic acid and itaconic acid is completely different, the effect of reduced oxygen transfer rates will likely differ.

To rule out this effect, we evaluated U. trichophora TZ1 in more industrially relevant conditions. To this end, it was cultivated in a bioreactor with MTM containing 200 g L−1 crude glycerol and 3.2 g L−1 NH4Cl. The pH was kept stable at 6.5 by automatic addition of NaOH. Additional crude glycerol was fed upon glycerol depletion (Fig. 6).

Fig. 6
figure 6

Fermentation of Ustilago trichophora TZ1 with crude glycerol. Malate concentration (red, squares), glycerol concentration (blue, circles) and OD600 (green, triangles) in MTM containing 200 g L−1 crude glycerol, 3.2 g L−1 NH4Cl at 28 °C (37 °C during production phase, 48 h) with DO kept at 30 %. pH was kept at 6.5 by automatic addition of NaOH. Shown is one exemplary fermentation run

This fermentation resulted in OD600 values and growth rates comparable to the ones in bioreactors with pharma-grade glycerol. Also the glycerol uptake rate (2.90 g L−1 h−1) and the malic acid production rate (0.75 g L−1) were comparable to the ones with pharma-grade glycerol. Only the yield was lowered to 0.26 g g−1. A slight negative impact of crude glycerol compared to pharma-grade glycerol on organic acid production has already been shown for Yarrowia lipolytica in citric acid production [52]. Interestingly, for U. trichophora TZ1 the accumulation of impurities by glycerol feed adding up to 476 g glycerol did not result in lowered production properties, which hints at an effect which is perhaps limited to the initial growth phase. A possibility to overcome this issue would be a second adaptive laboratory evolution on crude glycerol. For this, however, it has to be taken into consideration that depending on the origin of the crude glycerol, the composition of contained impurities differs in a broad range, not only in concentration, but also in components themselves [53]. In addition, to the already high tolerance to impurities in crude glycerol by U. trichophora TZ1 and thus only slight negative effect, the contained salts might also have a beneficial effect. For Actinobacillus succinogenes, it could be shown that synthetic seawater can act as mineral supplement [54].


The strain U. trichophora TZ1, which recently has been reported as promising production organism for malate from glycerol, is capable of producing 200 g L−1 malic acid at an overall rate of 0.74 g L−1 h−1 reaching a maximal production rate of 1.94 g L−1 h−1 and a yield of 0.31 mol mol−1 (31 % of the theoretical maximum assuming CO2 co-fixation or 41 % assuming no CO2 co-fixation) in bioreactors. These values, which are some of the highest reported for microbial malic acid production, allow U. trichophora TZ1, though only having undergone adaptive laboratory evolution and medium and fermentation optimization, to compete with highly engineered strains overexpressing major parts of the malate production pathway. Thus, further optimization of U. trichophora TZ1 could focus on metabolic engineering, which would not only harbor considerable potential to increase the production rate but also allow for strain optimization in terms of product to substrate yield by targeted disruption of by-product formation pathways. A subsequent systems biology comparison between the wild-type and the evolved strain not only could shed light on the adaptational mutations that enhanced the growth and production rate of U. trichophora TZ1 on glycerol but might also provide insights into why the strain utilizes glycerol faster than other Ustilaginaceae. In addition, it could clarify the glycerol uptake and degradation pathway and expand the general knowledge base of this relatively obscure Ustilago strain. This would clearly help to develop it into a platform for the production of not only malate but also other industrially relevant chemicals, to be produced from biodiesel-derived crude glycerol.


Strains and culture conditions

Ustilago trichophora TZ1 was used throughout this study [18].

As standard medium, modified Tabuchi medium (MTM) according to Geiser et al. containing 0.2 g L−1 MgSO4 7 H2O, 10 mg L−1 FeSO4 7 H2O, 0.5 g L−1 KH2PO4, 1 mL L−1 vitamin solution, 1 mL L−1 trace element solution [17] and differing concentrations of NH4Cl and (crude) glycerol was used. For additional glycerol feeds, 200 mL of an 800 g L−1 glycerol solution was added to the cultures. Additional 150 g CaCO3 was fed to the cultures as solids, when the pH value dropped below 5.5. Pharma-grade glycerol was used for all cultures except for those where the use of crude glycerol is explicitly stated. Crude glycerol was used as 80 % (w/v) aqueous solution and autoclaved without prior purification. After addition of all medium components, the pH value was adjusted to 6.5.

All batch cultivations were performed in New Brunswick BioFlo® 110 bioreactors (Eppendorf, Germany) with a total volume of 2.5 L and a working volume of 1.25 L. Temperature was maintained at 30 °C and the pH value was either set to 6.5 and controlled automatically with 10 M NaOH or different amounts of CaCO3 were added as buffer. To prevent foam formation, antifoam 204 (Sigma Life Science, USA) was added automatically using level sensor control. The aeration rate was set to 1.25 L min−1 (1 vvm) and the dissolved oxygen tension (DOT) was kept at 80 % saturation by automatically adjusting the stirring rate. As preculture, 50 mL MTM containing 0.8 g L−1 NH4Cl, 50 g L−1 glycerol, and 100 mM MES in 500-mL shake flasks was inoculated from an overnight YEP culture to an OD600 of 0.5. This culture was grown over night, washed twice by dissolving the pelleted cells (5000 rpm, 5 min, 30 °C) in 10 mL distilled water and used for inoculation of the bioreactor to an initial OD600 of 0.5. All shake flask cultures were incubated at 30 °C (relative air humidity = 80 %) shaking at 200 rpm (shaking diameter = 25 mm).

Analytical methods

All experiments were performed in duplicates. Shown is the arithmetic mean of the duplicates. Error bars and ±values indicate deviation from the mean.

From bioreactors, 5 mL of culture broth was taken for OD600 and HPLC analysis. When using CaCO3 as buffer, the CaCO3 in 1 mL culture broth was dissolved with HCl prior to further measurements. OD600 was determined in an Ultrospec 10 cell density meter (Amersham Biosciences, UK); samples were diluted to an OD600 between 0.1 and 0.8.

For HPLC analysis, centrifuged samples (13.000g, 5 min) were filtered through cellulose acetate filters (diameter 0.2 µm, VWR, Germany) prior to diluting 1:10 with distilled water. For analysis of glycerol and organic acids, a Dionex Ultimate 3000 HPLC (Dionex, USA) was used with an Organic Acid Resin column (CS-Chromatographie, Germany) at 75 °C, with a constant flow rate of 0.8 mL min−1 5 mM sulfuric acid as eluent. For detection, a Shodex RI 101 detector at 35 °C and a variable wavelength UV detector (Dionex, USA) at 210 nm were used.

Ammonium concentration was determined by a colorimetric assay according to Willis [55].

Calculation of the molar fraction of undissociated and dissociated species for malate was performed using CurTiPot [56].



Modified Tabuchi medium


2-(N-morpholino)ethanesulfonic acid


High-performance liquid chromatography


  1. Anand P, Saxena RK. A comparative study of solvent-assisted pretreatment of biodiesel derived crude glycerol on growth and 1,3-propanediol production from Citrobacter freundii. New Biotechnol. 2012;29(2):199–205.

    Article  CAS  Google Scholar 

  2. Yang F, Hanna MA, Sun R. Value-added uses for crude glycerol—a byproduct of biodiesel production. Biotechnol Biofuels. 2012;5:13.

    Article  CAS  Google Scholar 

  3. West TP. Crude glycerol: a feedstock for organic acid production by microbial bioconversion. J Microbial Biochem Technol. 2012;4:ii–ii. doi:10.4172/1948-5948.1000e106.

  4. Nicol RW, Marchand K, Lubitz WD. Bioconversion of crude glycerol by fungi. Appl Microbiol Biotechnol. 2012;93(5):1865–75.

    Article  CAS  Google Scholar 

  5. Goldberg I, Rokem JS, Pines O. Organic acids: old metabolites, new themes. J Chem Technol Biotechnol. 2006;81(10):1601–11.

    Article  CAS  Google Scholar 

  6. Sauer M, Porro D, Mattanovich D, Branduardi P. Microbial production of organic acids: expanding the markets. Trends Biotechnol. 2008;26(2):100–8.

    Article  CAS  Google Scholar 

  7. Werpy T, Petersen GR, Aden A, Bozell JJ, Holladay J, White J, Manheim A, Eliot D, Lasure L, Jones S. Top value added chemicals from biomass. Volume 1—Results of screening for potential candidates from sugars and synthesis gas; 2004; US-DoE Report PNNL-16983.

  8. Battat E, Peleg Y, Bercovitz A, Rokem JS, Goldberg I. Optimization of l-malic acid production by Aspergillus flavus in a stirred fermentor. Biotechnol Bioeng. 1991;37(11):1108–16.

    Article  CAS  Google Scholar 

  9. Knuf C, Nookaew I, Remmers I, Khoomrung S, Brown S, Berry A, Nielsen J. Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68. Appl Microbiol Biotechnol. 2014;98(8):3517–27.

    Article  CAS  Google Scholar 

  10. Peleg Y, Stieglitz B, Goldberg I. Malic acid accumulation by Aspergillus flavus. Appl Environ Microbiol. 1988;28:69–75.

    CAS  Google Scholar 

  11. Abe S, Furuya A. Method of producing l-malic acid by fermentation. 1962; Patent US3063910.

  12. Magnuson JK, Lasure LL. Organic acid production by filamentous fungi. In: Tkacz JS, Lange L, editors. Advances in fungal biotechnology for industry, agriculture and medicine. Springer: New York; 2004. p. 307–40.

    Chapter  Google Scholar 

  13. Moon SY, Hong SH, Kim TY, Lee SY. Metabolic engineering of Escherichia coli for the production of malic acid. Biochem Eng J. 2008;40(2):312–20.

    Article  CAS  Google Scholar 

  14. Zhang X, Wang X, Shanmugam KT, Ingram LO. l-malate production by metabolically engineered Escherichia coli. Appl Environ Microbiol. 2011;77(2):427–34.

    Article  CAS  Google Scholar 

  15. Zelle RM, de Hulster E, van Winden WA, de Waard P, Dijkema C, Winkler AA, Geertman JM, van Dijken JP, Pronk JT, van Maris AJ. Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl Environ Microbiol. 2008;74(9):2766–77.

    Article  CAS  Google Scholar 

  16. Brown SH, Bashkirova L, Berka R, Chandler T, Doty T, McCall K, McCulloch M, McFarland S, Thompson S, Yaver D, et al. Metabolic engineering of Aspergillus oryzae NRRL 3488 for increased production of L-malic acid. Appl Microbiol Biotechnol. 2013;97(20):8903–12.

    Article  CAS  Google Scholar 

  17. Geiser E, Wiebach V, Wierckx N, Blank LM. Prospecting the biodiversity of the fungal family Ustilaginaceae for the production of value-added chemicals. BMC Fungal Biol Biotechnol. 2014;1:2.

    Article  Google Scholar 

  18. Zambanini T, Sarikaya E, Kleineberg W, Buescher JM, Meurer G, Wierckx N, Blank LM. Efficient malic acid production from glycerol with Ustilago trichophora TZ1. Biotechnol Biofuels. 2016;9(1):1–8.

    Article  Google Scholar 

  19. Maassen N, Panakova M, Wierckx N, Geiser E, Zimmermann M, Bölker M, Klinner U, Blank LM. Influence of carbon and nitrogen concentration on itaconic acid production by the smut fungus Ustilago maydis. Eng Life Sci. 2013;14(2):129–34.

    Article  Google Scholar 

  20. Klement T, Büchs J. Itaconic acid—a biotechnological process in change. Bioresour Technol. 2013;135:422–31.

    Article  CAS  Google Scholar 

  21. Feldbrügge M, Kellner R, Schipper K. The biotechnological use and potential of plant pathogenic smut fungi. Appl Microbiol Biotechnol. 2013;97(8):3253–65.

    Article  Google Scholar 

  22. Bölker M, Basse CW, Schirawski J. Ustilago maydis secondary metabolism—from genomics to biochemistry. Fungal Genet Biol. 2008;45:88–93.

    Article  Google Scholar 

  23. Guevarra ED, Tabuchi T. Accumulation of itaconic, 2-hydroxyparaconic, itatartaric, and malic acids by strains of the genus Ustilago. Agr Biol Chem Tokyo. 1990;54(9):2353–8.

    CAS  Google Scholar 

  24. Jeya M, Lee KM, Tiwari MK, Kim JS, Gunasekaran P, Kim SY, Kim IW, Lee JK. Isolation of a novel high erythritol-producing Pseudozyma tsukubaensis and scale-up of erythritol fermentation to industrial level. Appl Microbiol Biotechnol. 2009;83(2):225–31.

    Article  CAS  Google Scholar 

  25. Moon HJ, Jeya M, Kim IW, Lee JK. Biotechnological production of erythritol and its applications. Appl Microbiol Biotechnol. 2010;86(4):1017–25.

    Article  CAS  Google Scholar 

  26. Giese H, Azizan A, Kummel A, Liao A, Peter CP, Fonseca JA, Hermann R, Duarte TM, Buchs J. Liquid films on shake flask walls explain increasing maximum oxygen transfer capacities with elevating viscosity. Biotechnol Bioeng. 2014;111(2):295–308.

    Article  CAS  Google Scholar 

  27. Gyamerah MH. Oxygen requirement and energy relations of itaconic acid fermentation by Aspergillus terreus NRRL 1960. Appl Microbiol Biotechnol. 1995;44(1–2):20–6.

    Article  Google Scholar 

  28. Klement T, Milker S, Jäger G, Grande PM, de Maria PD, Büchs J. Biomass pretreatment affects Ustilago maydis in producing itaconic acid. Microb Cell Fact. 2012;11:43.

    Article  CAS  Google Scholar 

  29. Morita T, Fukuoka T, Imura T, Kitamoto D. Production of glycolipid biosurfactants by basidiomycetous yeasts. Biotechnol Appl Biochem. 2009;53:39–49.

    Article  CAS  Google Scholar 

  30. Hewald S, Linne U, Scherer M, Marahiel MA, Kämper J, Bölker M. Identification of a gene cluster for biosynthesis of mannosylerythritol lipids in the basidiomycetous fungus Ustilago maydis. Appl Environ Microbiol. 2006;72(8):5469–77.

    Article  CAS  Google Scholar 

  31. Teichmann B, Linne U, Hewald S, Marahiel MA, Bolker M. A biosynthetic gene cluster for a secreted cellobiose lipid with antifungal activity from Ustilago maydis. Mol Microbiol. 2007;66(2):525–33.

    Article  CAS  Google Scholar 

  32. Geiser E. Itaconic acid production by Ustilago maydis, vol. 1. Aachen: Apprimus; 2015.

    Google Scholar 

  33. Duskova M, Borovikova D, Herynkova P, Rapoport A, Sychrova H. The role of glycerol transporters in yeast cells in various physiological and stress conditions. FEMS Microbiol Lett. 2015;362(3):1–8.

    Article  Google Scholar 

  34. Duskova M, Ferreira C, Lucas C, Sychrova H. Two glycerol uptake systems contribute to the high osmotolerance of Zygosaccharomyces rouxii. Mol Microbiol. 2015;97(3):541–59.

    Article  CAS  Google Scholar 

  35. Guevarra ED, Tabuchi T. Production of 2-hydroxyparaconic and itatartaric acids by Ustilago cynodontis and simple recovery process of the acids. Agric Biol Chem Tokyo. 1990;54(9):2359–65.

    CAS  Google Scholar 

  36. Kuenz A. Itaconsäureherstellung aus nachwachsenden Rohstoffen als Ersatz für petrochemisch hergestellte Acrylsäure. Dissertation. Braunschweig: Technischen Universität Carolo-Wilhelmina Braunschweig, Germany; 2008.

  37. Park Y, Ohta N, Okabe M. Effect of dissolved oxygen concentration and impeller tip speed on itaconic acid production by Aspergillus terreus. Biotechnol Lett. 1993;15(6):583–6.

    Article  CAS  Google Scholar 

  38. Yahiro K, Takahama T, Park YS, Okabe M. Breeding of Aspergillus terreus mutant TN-484 for itaconic acid production with high yield. J Ferment Bioeng. 1995;79(5):506–8.

    Article  CAS  Google Scholar 

  39. Hevekerl A, Kuenz A, Vorlop K-D. Filamentous fungi in microtiter plates—an easy way to optimize itaconic acid production with Aspergillus terreus. Appl Microbiol Biotechnol. 2014:98(16):6983–9.

  40. Yuzbashev TV, Yuzbasheva EY, Sobolevskaya TI, Laptev IA, Vybornaya TV, Larina AS, Matsui K, Fukui K, Sineoky SP. Production of succinic acid at low pH by a recombinant strain of the aerobic yeast Yarrowia lipolytica. Biotechnol Bioeng. 2010;107(4):673–82.

    Article  CAS  Google Scholar 

  41. Yuzbashev TV, Yuzbasheva EY, Laptev IA, Sobolevskaya TI, Vybornaya TV, Larina AS, Gvilava IT, Antonova SV, Sineoky SP. Is it possible to produce succinic acid at a low pH? Bioeng Bugs. 2011;2(2):115–9.

    Article  Google Scholar 

  42. Amy HAM, Berovic M, Gluszca P, Kristiansen B, Krzystek L, Kubicek C, Ledakowicz S, Lesniak W, Mattey M, Papagianni M et al. Citric acid biotechnology. In. Kristiansen B, Mattey M, Linden J, editors. Taylor & Francis e-Library; 2002.

  43. Wu J, Peng Q, Arlt W, Minceva M. Model-based design of a pilot-scale simulated moving bed for purification of citric acid from fermentation broth. J Chromatogr A. 2009;1216(50):8793–805.

    Article  CAS  Google Scholar 

  44. Adams Jr. F, Rice LF, Taylor RJ. Itaconic acid purification process using reverse osmosis. 1970; Patent US3544455.

  45. van Maris AJ, Konings WN, van Dijken JP, Pronk JT. Microbial export of lactic and 3-hydroxypropanoic acid: implications for industrial fermentation processes. Metab Eng. 2004;6(4):245–55.

    Article  Google Scholar 

  46. Abbott DA, Zelle RM, Pronk JT, van Maris AJ. Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids: current status and challenges. FEMS Yeast Res. 2009;9(8):1123–36.

    Article  CAS  Google Scholar 

  47. Jamalzadeh E, Verheijen PJ, Heijnen JJ, van Gulik WM. pH-dependent uptake of fumaric acid in Saccharomyces cerevisiae under anaerobic conditions. Appl Environ Microbiol. 2012;78(3):705–16.

    Article  CAS  Google Scholar 

  48. Jamalzadeh E, Taymaz-Nikerel H, Heijnen JJ, van Gulik WM, Verheijen PJT. A thermodynamic analysis of dicarboxylic acid production in microorganisms. In: von Stockar U, van der Wielen LAM, Prausnitz JM, editors. Thermodynamics in biochemical engineering. Switzerland: Lausanne; 2012.

    Google Scholar 

  49. Dobson R, Gray V, Rumbold K. Microbial utilization of crude glycerol for the production of value-added products. J Ind Microbiol Biotechnol. 2012;39(2):217–26.

    Article  CAS  Google Scholar 

  50. Morgan MJ, Lehmann M, Schwarzländer M, Baxter CJ, Sienkiewicz-Porzucek A, Williams TC, Schauer N, Fernie AR, Fricker MD, Ratcliffe RG, et al. Decrease in manganese superoxide dismutase leads to reduced root growth and affects tricarboxylic acid cycle flux and mitochondrial redox homeostasis. Plant Physiol. 2008;147(1):101–14.

    Article  CAS  Google Scholar 

  51. Anastassiadis S, Aivasidis A, Wandrey C. Citric acid production by Candida strains under intracellular nitrogen limitation. Appl Microbiol Biotechnol. 2002;60(1–2):81–7.

    CAS  Google Scholar 

  52. Rymowicz W, Rywinska A, Marcinkiewicz M. High-yield production of erythritol from raw glycerol in fed-batch cultures of Yarrowia lipolytica. Biotechnol Lett. 2009;31(3):377–80.

    Article  CAS  Google Scholar 

  53. Samul D, Leja K, Grajek W. Impurities of crude glycerol and their effect on metabolite production. Ann Microbiol. 2014;64:891–8.

    Article  CAS  Google Scholar 

  54. Lin CSK, Luque R, Clark JH, Webb C, Du C. A seawater-based biorefining strategy for fermentative production and chemical transformations of succinic acid. R Soc Chem Adv. 2011;4(4):1471–9.

    CAS  Google Scholar 

  55. Willis RB, Montgomery ME, Allen PR. Improved method for manual, colorimetry determination of total Kjeldahl nitrogen using salicylate. J Agric Food Chem. 1996;44(7):1804–7.

    Article  CAS  Google Scholar 

  56. CurTiPot. pH and acid-base titration curves: analysis and simulation freeware, version 4.2. 23 May 2016.

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Authors’ contributions

LMB, NW, and GM conceived and designed the project. TZ, NW, JMB, and LMB designed experiments and analyzed results. TZ and NW wrote the manuscript with the help of LMB and JMB. TZ, WK, and ES performed the experiments. All authors read and approved the final manuscript.


We thank Elena Geiser for technical assistance and valuable discussion. We gratefully acknowledge BioEton for providing the (crude) glycerol.

Competing interests

GM and JMB are paid employees of BRAIN AG. The authors declare that no financial or non-financial conflict of interest was present with regard to the results or interpretation of the reported experiments. Further, they declare that this does not alter the permission of unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


This study was partially funded by the Biotechnology Research And Information Network AG (BRAIN AG) and by the German Federal Ministry of Education and Research (BMBF) as part of the Strategic Alliance ZeroCarbFP (Grant No. FKZ 031A217F).

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Correspondence to Nick Wierckx.

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Zambanini, T., Kleineberg, W., Sarikaya, E. et al. Enhanced malic acid production from glycerol with high-cell density Ustilago trichophora TZ1 cultivations. Biotechnol Biofuels 9, 135 (2016).

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