1. Introduction
In recent years, there has been a significant focus on producing bio-based fuels and chemicals as sustainable alternatives to petrochemicals. Syngas fermentation, a burgeoning field of research, is one of the promising alternatives [
1,
2,
3]. In syngas fermentation, gas mixtures of CO, H
2, and CO
2 are converted by anaerobic microorganisms into short chain organic acids and alcohols, which can subsequently be used as bio-based products [
4,
5,
6]. Biogenic syngas can be produced by gasifying waste biomass, dried green waste, or corn cobs [
4,
7,
8]. Additionally, syngas is obtained from CO-rich waste gas emitted during industrial processes, such as steel production [
4,
9]. The main components of syngas are CO, CO
2, H
2, and N
2 [
10,
11,
12]. The advantages of syngas fermentation include its ability to occur in water under mild reaction conditions, such as 30 – 37°C and low pressure, as well as the low costs of the self-regenerating biocatalysts [
4]. Moreover, these microbes can adapt to a wide range of syngas compositions and exhibit tolerance to various impurities, including sulfur-containing compounds [
13,
14].
Unicarbonotrophic, acetogenic anaerobes such as
Clostridium autoethanogenum, Clostridium ljungdahlii, and
Clostridium ragsdalei can conserve energy and assimilate carbon through the reductive acetyl coenzyme A (Acetyl-CoA) pathway, also known as the Wood-Ljungdahl pathway (WLP). The required electrons are derived either from CO or H
2, whereas CO is thermodynamically favored over H
2 [
15]. Acetyl-CoA, the key intermediate, is generated through a series of reduction reactions, and is then available for anabolism and product formation [
16,
17,
18]. The acetyl-CoA is formed by consuming adenosine triphosphate (ATP) [
1]. This ATP consumption, resulting through the formyl-tetrahydrofolate-synthase, can be offset through either substrate-level phosphorylation, when acetyl-phosphate reacts to acetate by the acetate kinase, or by a membrane-bound ATPase driven by a membrane-bound Rnf complex [
1,
19].
The aforementioned strictly anaerobic bacteria produce acetate, ethanol, and 2,3-butanediol, whereas
C. carboxidivorans has the additional ability to produce butyrate, 1-butanol, hexanoate, and 1-hexanol. However, the concentrations of the C4-C6 products remain low, and the production of acids is not particularly favorable [
20,
21,
22].
C. autoethanogenum, being an extensively studied and sequenced acetogen, is already employed for the industrial production of ethanol from steel-mill off-gases [
10,
23,
24].
However, the challenges in syngas fermentation remain the low solubilities of H
2 and CO in water, which may result in gas-liquid mass transfer limitations, the poor alcohol-to-acid ratios and low product concentrations with wild-type strains, and the low biomass densities in submerged syngas fermentation resulting in low volumetric productivities [
25]. Therefore, various studies have investigated the optimization of autotrophic cultivation conditions, including partial pressures of the syngas components (nutrient level), pressure, pH, medium composition, and temperature [
4,
13,
26,
27]. For instance,
Clostridium aceticum can utilize CO as a sole source of carbon and energy. However, its ability to withstand higher concentrations of CO is limited [
28]. In contrast,
C. autoethanogenum shows a higher tolerance to increased CO levels [
15,
26]. Further studies focused on genetically engineered
C. autoethanogenum and showed enhanced autotrophic growth and product formation [
29,
30,
31,
32,
33,
34]. Liew et al. [
30] discovered that the presence of the CO dehydrogenase isogene acsA is crucial for autotrophic growth, while deleting it actually increased product formation. Additionally, novel product routes to value-added molecules, such as 3-hydroxypropionate, 1-propanol, and acetone, have been introduced by applying metabolic engineering [
35].
As the aforementioned strategies only lead to limited improvements in the autotrophic formation of products with increased carbon chain lengths (> C2), further strategies are required [
4,
33,
36,
37]. For example, co-cultivation of anaerobic microorganisms can form longer-chain alcohols and organic acids, for instance, 1-hexanol and hexanoate, with higher added value through chain elongation [
38,
39,
40,
41,
42]. In a study by Diender et al. [
38], a concentration of hexanoate reaching 1.2 g L
-1 was achieved through the autotrophic co-culture of
C. autoethanogenum and the chain elongator
C. kluyveri. However, the low amount of autotrophic ethanol production remains a limiting factor for chain elongation by
C. kluyveri. Continuous processes have been studied to enable higher volumetric productivities in syngas fermentations, e.g. continuous stirred-tank bioreactors and cascades thereof, membrane reactors enabling cell retention as well as biofilm reactors [
33,
39,
43,
44,
45,
46,
47]. For instance, Mayer et al. [
28] achieved a CO conversion of 70% with
C. aceticum in a continuously operated stirred-tank bioreactor with a novel submerged microfiltration membrane module that enables total cell retention.
Apart from the WLP, in which anaerobia metabolize autotrophic substrates, they can also consume heterotrophic substrates via the Embden-Meyerhof-Parnas (EMP) pathway (glycolysis) [
1,
19,
48,
49]. For instance,
Clostridium magnum grows with a broad spectrum of pentoses, hexoses, glycerol, cellobiose, and maltodextrin, respectively, whereas
C. autoethanogenum can only use a very limited range of carbohydrates, particularly D-fructose, D-xylose, L-arabinose, and D-ribose, to a lesser extent [
23,
50]. Hereby, D-xylose and L-arabinose are of particular interest as these pentoses can easily be produced by acid-catalyzed or enzymatic hydrolysis of residual lignocellulosic biomass, such as straw or extracted sugar beet press pulp [
51,
52,
53].
In two degradation steps, D-fructose is integrated into glycolysis, forming ẞ-D-fructose-1,6-bisphosphate. However, implementing L-arabinose and D-xylose into the glycolysis is significantly more complex. In the first step, the sugars are activated to either D-xylose phosphate or L-ribose phosphate. These intermediates are then incorporated into the pentose phosphate pathway (PPP) and degraded to ẞ-D-fructose-6-phosphate or glyceraldehyde-3-phosphate through several intermediate steps. These metabolites can be assembled into glycolysis and reduced to the central intermediate acetyl-CoA. [
19,
54,
55,
56]. Aristilde et al. [
56] demonstrated with
Clostridium acetobutylicum that D-xylose and L-arabinose can also be metabolized via a glycolysis-independent pathway, the phosphoketolase pathway (PKP). However, many questions remain unanswered regarding elucidating metabolic pathways, regulatory mechanisms, and the evaluation of product formation.
Compared to the WLP, glycolysis can generate ATP. But if, for example, hexose is used as a carbon source for fermentation, two-third of the available carbon can be utilized for growth and product formation, whereas the remaining one-third is oxidized to CO
2 during pyruvate decarboxylation [
1,
48]. However, providing autotrophic and heterotrophic carbon sources simultaneously leads to a biomass yield improvement and is a promising strategy to overcome the limits in autotrophic syngas fermentation. This concept is also known as non-photosynthetic or acetogenic mixotrophy [
1,
48,
49,
57]. Previous studies have already shown that several
Clostridia can metabolize C1 and C5 or C6 molecules simultaneously. Maru et al. [
50] studied 17 acetogens to determine their organic and inorganic carbon substrate utilization. Their findings indicate that mixotrophy leads to increased biomass and product yields. The carbon yields of
Thermoanaerobacter kivui and
Blautia producta approached nearly 100% carbon fixation in acetate, lactate, and ethanol. Furthermore,
C. ljungdahlii was genetically modified to ensure that D-glucose was not preferentially but rather simultaneously consumed with syngas. Jones et al. [
48] reported the production of acetone using a genetically modified strain of
C. ljungdahlii, achieving an acetone yield of 92% of the theoretical maximum for mixotrophic conditions with D-fructose. Through C
13-labeling of the carbons in the syngas, it was shown that 70% of the acetate was formed from syngas at the maximum. In another study,
C. carboxidivorans utilized 10 g L
-1 D-Glucose and a gas mixture with 20%CO, resulting in enhanced alcohol concentrations of up to 9.1 g L
-1 in the batch process [
58].
A study by Mann et al. [
59] has already shown that higher CO conversion can be achieved by the simultaneous utilization of D-xylose and gaseous carbon substrates in a fed-batch process with
C. autoethanogenum. In contrast, Abubackar et al. [
60] reported reduced CO utilization of
C. autoethanogenum in the presence of D-xylose in a STR at pH 5.75. Jones et al. [
48] showed simultaneous utilization of 10 g L
-1 D-fructose and a syngas mixture of
13CO:H
2:
13CO
2:N
2 (55:20:10:15) in anaerobic flasks with
C. autoethanogenum. 51-58% of acetate was produced from syngas during the whole batch processes; however, ethanol was not measured.
Oliveira et al. [
61] compared the ability of
C. autoethanogenum,
C. ljungdahli, and
C. ragsdalei to convert CO-rich syngas in autotrophic batch processes. Among the three strains,
C. autoethanogenum demonstrated the highest final ethanol and D-2,3-butanediol concentrations and achieved a final alcohol-to-acetate ratio of 7.6 (w/w). As shown before, mixotrophic fermentation processes are promising but sparsely investigated so far with
C. autoethanogenum. The published results were achieved at uncontrolled reaction conditions in most of the cases, as well as with insufficient and incomplete product analytics with no data on gas consumption or production rates. It remains unclear how the ratio of varying sugar sources to syngas affects the simultaneous carbon utilization and formation of products. Consequently, we first investigate the batch conversion of varying initial concentrations of the two pentoses D-xylose and L-arabinose on growth, product formation, and gas uptake or formation rates with
C. autoethanogenum under mixotrophic conditions in a fully controlled stirred-tank reactor with continuous gassing. L-arabinose has not been used before under mixotrophic conditions with
C. autoethanogenum. That is why we opted for an appropriate initial concentration of L-arabinose. Mixotrophic batch processes with the hexose D-fructose are studied as well.
2. Materials and Methods
2.1. Microorganism, Medium, and Heterotrophic Preculture Preparation
C. autoethanogenum JA1-1 (DSM 10061) was purchased from the German Collection of Microorganisms and Cell Culture (DSMZ, Braunschweig, Germany) as freeze-dried cultures.
The preparation, sterilization, and anaerobization of the media for preculture and reactor cultivation were performed, as reported by Rückel et al. [
62]. The composition of the media is listed in the
Supporting Information (Table S1).
For the preculture preparations of the reference batch process, 2.5 mL of a stored cryopreserved cell broth of C. autoethanogenum with ~ 0.05 g L-1 cell dry weight (CDW) was added to sterile anaerobic 250 mL flasks with 100 mL medium. 5 g L-1 D-xylose was used as a heterotrophic carbon source, and 0.4 g L-1 cysteine hydrochloride was added as a reducing agent. 5 g L-1 of either D-xylose, L-arabinose, or D-fructose was applied for the mixotrophic preculture preparations.
The anaerobic flasks were incubated for 22 h at 37°C and 100 min-1 in an incubator (WIS-20, Witeg, Wertheim, Germany). C. autoethanogenum was harvested at the end of the exponential growth phase by centrifugation (10 min, 3620 rcf, Rotica 50 RS, Hettich GmbH & Co. KG, Tuttlingen, Germany) under anaerobic conditions. The separated cells were resuspended with 10 mL anaerobic phosphate-buffered saline (12 mM phosphate) before inoculation of the stirred-tank bioreactor.
2.2. Continuously Gassed Stirred-Tank Bioreactor Setup
All batch cultivations were carried out under continuous gas supply in a fully controlled stainless steel, stirred-tank bioreactor (STR) (KLF2000, Bio-Engineering, Wald, Switzerland). The nominal volume was 2.4 L (dtank = 98 mm) with a working volume of 1 L. The STR was agitated with two six-blade Rushton turbines. A temperature sensor, a heating, and a cooling rod were used for temperature control. A sterilizable pH sensor (405-DPAS-SC-K8s/120, Mettler Toledo, Germany) and a sterilizable redox sensor (Pt4805-DPAS-SC-K8S/120, Mettler Toledo, Germany) were inserted through two side ports of the STR. 3 M NaOH or 0.5 M H2SO4 were added via two lid ports for pH-control. A pressure probe and a safety valve were installed at the lid as well. A tube was fixed at the baffles inside the STR for the syngas supply via the lid to a sintered frit below the stirrer at the bottom of the reactor. An exhaust gas section guides the reactor off-gas out of the STR. By cooling the off-gas at 2°C, evaporation is reduced. A sampling valve was installed at the bottom of the STR.
The STR was sterilized
in situ at 121°C for 21 min at 2.2 bar absolute pressure with 1 L medium (without vitamins, L-cysteine hydrochloride, heterotrophic carbon source, and MES). After cooling to 37°C, 10 mL of vitamin stock solution was added aseptically through a syringe filter with 0.2 µm pore size via a septum (diameter 12 mm, Infors AG, Bottmingen, Switzerland) fixed in a lid inlet. The detailed compositions of the vitamin stock solution are in the
Supporting Information (Table S1). The medium was anaerobized for approximately 2 h with 20 NL h
-1 N
2 and afterward saturated with 5 NL h
-1 of the syngas mixture for at least 16 h.
Heterotrophic carbon sources were added immediately before inoculation. Therefore, anaerobic, sterile stock solutions were prepared with either 250 g L-1 D-xylose, 200 g L-1 L-arabinose, or 375 g L-1 D-fructose. The volume for achieving initial concentrations of 10 g L-1, 15 g L-1, or 20 g L-1 of the varying heterotrophic carbon sources in the STR were added through a septum with single-use syringes (BD Discardit II, Becton Dickinson, Franklin Lakes, NJ, USA) and sterile needles (Sterican 0.9 x 70 mm, B. Braun, Melsungen, Germany). 10 mL of 40 g L-1 L-cysteine hydrochloride stock solution was finally added as a reducing agent before inoculation with C. autoethanogenum to achieve an initial cell dry weight concentration of 0.03 g L-1.
All batch processes were performed at a constant stirrer speed of 1200 rpm (volumetric power input of 15.1 W L-1). The temperature was controlled at 37°C, and the pH was kept at pH 6.0. The batch cultivations were carried out at 1 bar absolute pressure. The STR was continuously gassed with 5 NL h-1 (0.083 vvm).
An artificial syngas mixture was prepared using a gas mixing system with four thermal mass flow controllers (P-702CV-6K0R-RAD-33-V, Bronkhorst, Reinach, Switzerland). The flow rates of the syngas components were adjusted to 1.95 NL h-1 (pN2 = 390 mbar) N2, 1.50 NL h-1 (pCO = 300 mbar) CO, 1.10 NL h-1 (pH2 = 220 mbar) H2, and 0.45 NL h-1 (pCO2 = 90 mbar) CO2. The flow rates of the heterotrophic batch process were adjusted to 4.55 NL h-1 (pN2 = 910 bar) N2 and 0.45 NL h-1 (pCO2 = 90 bar) CO2.
2.3. Analytical Methods
During the batch processes, liquid samples for biomass and product concentrations were collected via the sampling valve on the bottom of the STR.
The samples’ optical density (OD
600) was measured at 600 nm in a UV-Vis spectrophotometer (Genesys 10S UV-Vis, Thermo Scientific, Neuss, Germany). The measurements of OD
600 were carried out in technical triplicates for each sample. In general, the biomass concentration was estimated based on the optical density with a correlation factor of 0.38 g L
-1 OD
-1 [
61,
62,
63].
The product concentrations (organic acids and alcohols) were analyzed with high-performance liquid chromatography (HPLC) (LC-2030C, Shimadzu, Kyoto, Japan). The HPLC analysis was performed using a cation exchange separation column (Aminex HPX-87H, Bio-Rad, Munich, Germany) and a refractive index detector (RID-20A, Shimadzu, Kyoto, Japan). All measurements were carried out under isocratic elution conditions at a constant flow rate of 0.6 mL min-1 5 mM H2SO4 and a column oven temperature of 60°C.
The volumetric exhaust gas flow rate was detected online with a thermal mass flow meter (MFM) (F-101D-RAD-33-V, Bronkhorst, Reinach, Switzerland) with a step time of 30 s. The off-gas composition of the syngas components N2, CO, CO2, and H2 was analyzed with a micro-gas chromatograph (µGC) (micro-GC 450, Agilent Technologies, Waldbronn, Germany). The µGC consists of three independent channels with thermal conductivity detectors and separation columns. With the first channel (molecular sieve, argon as a carrier gas, column temperature 80°C, initial pressure of 250 kPa), permanent gases like H2, N2, and CO can be identified. The second channel (PlotPQ, helium as carrier gas, column temperature 80°C, initial pressure of 150 kPa) can detect CO2, NH3, NOx. With channel 3 (CP-Sil 5, helium as carrier gas, column temperature 45°C, initial pressure 100 kPa), CO2 and H2S can be analyzed. Exhaust gas samples were analyzed with a step time of 12 minutes. The volumetric gas uptake and production rates of CO, CO2, and H2 were calculated based on the µGC-measured exhaust gas concentrations and the measured volumetric exhaust gas flow rates.