Upgrading Syngas Fermentation Effluent Using Clostridium Kluyveri in a Continuous Fermentation Sylvia Gildemyn1,2,4, Bastian Molitor1, Joseph G

Gildemyn et al. Biotechnol Biofuels (2017) 10:83 DOI 10.1186/s13068-017-0764-6 Biotechnology for Biofuels

RESEARCH Open Access Upgrading syngas fermentation effluent using Clostridium kluyveri in a continuous fermentation Sylvia Gildemyn1,2,4, Bastian Molitor1, Joseph G. Usack1, Mytien Nguyen1, Korneel Rabaey2 and Largus T. Angenent1,3*

Abstract Background: The product of current syngas fermentation systems is an ethanol/acetic acid mixture and the goal is to maximize ethanol recovery. However, ethanol currently has a relatively low market value and its separation from the fermentation broth is energy intensive. We can circumvent these disadvantages of ethanol production by converting the dilute ethanol/acetic acid mixture into products with longer carbon backbones, which are of higher value and are more easily extracted than ethanol. Chain elongation, which is the bioprocess in which ethanol is used to elongate short-chain carboxylic acids to medium-chain carboxylic acids (MCCAs), has been studied with pure cultures and open cultures of microbial consortia (microbiomes) with several different substrates. While upgrading syngas fermentation effluent has been studied with open cultures, to our knowledge, no study exists that has performed this with pure cultures. Results: Here, pure cultures of Clostridium kluyveri were used in continuous bioreactors to convert ethanol/acetic acid mixtures into MCCAs. Besides changing the operating conditions in regards to substrate loading rates and composition, the effect of in-line product extraction, pH, and the use of real syngas fermentation effluent on production rates were tested. Increasing the organic loading rates resulted in proportionally higher production rates of 1 1 1 n-caproic acid, which were up to 40 mM day− (4.64 g L− day− ) at carbon conversion efficiencies of 90% or higher. The production rates were similar for bioreactors with and without in-line product extraction. Furthermore, a lower ethanol/acetic acid ratio (3:1 instead of 10:1) enabled faster and more efficient n-caproic acid production. In addition, n-caprylic acid production was observed for the first time withC. kluyveri (up to 2.19 0.34 mM in batch). Finally, the use of real effluent from syngas fermentation, without added yeast extract, but± with added defined growth factors, did maintain similar production rates. Throughout the operating period, we observed that the metabolism of C. kluyveri was inhibited at a mildly acidic pH value of 5.5 compared to a pH value of 7.0, while reactor microbiomes perform successfully at mildly acidic conditions. Conclusions: Clostridium kluyveri can be used as a biocatalyst to upgrade syngas fermentation effluent into MCCAs at pH values above 5.5. Keywords: Chain elongation, Carboxylate platform, Syngas fermentation, Carboxylic acids, n-Caproic acid, n-Caprylic acid

Background awareness that the use of fossil fuels leads to climate The production of biochemicals as alternatives to fossil change and air pollution has resulted in the develop- fuel-based chemicals is gaining momentum. Increasing ment of several bioproduction routes [1]. First, with the sugar platform, the use of starch and sugar crops to pro- *Correspondence: l.angenent@uni‑tuebingen.de duce bioethanol currently results in production rates 3 University of Tübingen, Center for Applied GeoSciences, Hölderlinstr. 12, exceeding 60 g L−1 day−1 with commercial bioproduction 72074 Tübingen, Germany Full list of author information is available at the end of the article strains [2]. More than 100 million tons of bioethanol are

© The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 2 of 15

produced worldwide every year [3]. This platform is con- dissociation [18, 19]. At high dilution rates and neutral troversial because crop cultivation requires a high input pH, the maximum n-caproic acid production rate of of land, water, and nutrients [4]. Cultivation of these 55 g L−1 day−1 has been achieved [20]. crops for biofuel production may also compete with the Fourth, coupling different production platforms to production of food. Lignocellulosic biomass as feedstock upgrade side streams or produce higher value chemicals circumvents these issues but requires addition of chemi- could create additional value. For example, syngas fer- cals and process energy to pretreat the biomass to make mentation only leads to a marketable product when the the sugars available for fermentation, while a large per- fully miscible ethanol is extracted and separated from the centage of the biomass remains unused [1]. fermentation broth. Distillation of dilute ethanol (6% w/v Second, with the syngas platform, catalytic conver- in syngas fermentation effluent) is an energy-intensive sion of lignocellulosic biomass to syngas (H2/CO/CO2 process that results in a currently low-value product. gas mixtures), and subsequent autotrophic fermentation Mixtures of ethanol and acetic acid in syngas fermenta- of these gases to liquid products, could enable high car- tion effluent, in particular those with high ethanol/acetic bon efficiency while still avoiding crop-related concerns acid ratios, could also be further biologically converted to [5]. The syngas platform has potential because, in addi- MCCAs via chain elongation (Fig. 1) [21–23]. One of the tion to lignocellulosic biomass and other organic waste main questions is whether growth factors, such as trace streams, point sources of syngas are widely available such elements or yeast extract, would have to be added to the as the off-gases from steel manufacturing [6–8]. The use syngas fermentation effluent to enable the chain elonga- of industrial gaseous off streams can lead to decreased tion process, or if those already present in the effluent greenhouse gas emissions coupled to the production of would suffice to support growth. Addition of growth multicarbon products via fermentation, with ethanol factors would greatly increase the production cost for currently being the dominant product. Anaerobic auto- MCCAs. In two proof-of-concept studies that coupled trophic bacteria, such as C. ljungdahlii and C. autoetha- chain elongation to syngas fermentation, several growth nogenum, carry out this bioconversion. These bacteria factors, such as yeast extract, were added along with the utilize the Wood–Ljungdahl pathway for carbon fixation substrate. The necessity of these additions was, however, [9, 10]. The usual product of the autotrophic metabolism not studied [21, 22]. is acetic acid. When the intracellular, undissociated acetic acid concentration reaches a threshold, the metabolism is redirected towards ethanol production to decrease toxicity and increase the number of reducing equivalents per mole of product formed [11, 12]. Ethanol production rates exceeding 200 g L−1 day−1 are now obtainable with commercial strains [6]. Third, with the carboxylate platform, treatment of organic wastes is coupled to bioproduction via anaerobic fermentation processes. The carboxylate platform pri- marily involves the production of short-chain carboxylic acids (SCCAs) and gases, such as H2 and CO2, by utiliz- ing open cultures of microbial consortia (microbiomes) [13, 14]. Inhibition of methanogenesis, which is the last step in the anaerobic foodweb for biogas production, results in the buildup of SCCAs in the fermentation broth. Chain elongation via the reverse β-oxidation pathway then leads to the production of medium-chain carboxylic acids (MCCAs) within the microbiome [15, 16]. Among the end products, n-caproic acid and n-caprylic acid are two desirable MCCA bioproducts, but they are characterized by high product toxicities at mildly acidic Fig. 1 Simplified pathways showing the coupling of syngas fer- pH values (pKa ~4.8) [17]. Circumvention of product mentation, relying on the Wood–Ljungdahl pathway, and biological toxicity and high-rate fermentation can be achieved by chain elongation, relying on reverse β-oxidation. The red and green the following: (i) continuous removal of the produced box represents the boundary of the microorganism performing the carboxylic acids via in-line extraction; (ii) applying high pathway. More details on both pathways can be found in References dilution rates; or (iii) maintaining a favorable pH for acid [8] and [42] Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 3 of 15

The chain elongation process and its underlying ther- described, these carboxylic acids are fully or partially pre- modynamics are now well understood [23–25]. Several sent in their dissociated forms. microorganisms are known to convert ethanol/acetic acid mixtures via the reverse β-oxidation pathway, with Methods C. kluyveri being the most frequently studied microbe. C. Culture and media kluyveri has the ability to produce n-butyric and n-cap- A Clostridium kluyveri ATCC 8527 (DSM555) culture roic acid from ethanol and acetic acid [26], and has reg- was obtained from ATCC (Manassas, VA, USA) and ularly been found in microbiomes that converted either cultured according to the standard DSMZ protocols in synthetic or real organic waste streams into MCCAs [18, DSMZ52 medium. Only 1 mM cysteine was used as a 27]. Except for one study that determined substrate uti- reducing agent. The culture was incubated in serum flasks lization, pure-culture continuous bioreactor studies with at 35 °C without shaking. For bioreactor experiments, C. kluyveri are lacking [28]. Pure-culture fermentation MgSO4 was omitted from the medium and replaced with would allow more control of the chain elongation pro- an equimolar concentration of MgCl2·6H2O, while the cess. Furthermore, this would enable the investigation cysteine concentration was increased from 1 to 4 mM. In of different process parameters and their influence on addition, we adapted the concentrations of ethanol and the productivity of the culture. From studies of thermo- acetic acid to obtain the desired molar ratio of ethanol/ dynamic models and pure and open cultures it is known: acetic acid (10:1, later 3:1) and organic loading rate (OLR) (i) a higher ethanol/acetic acid ratio drives the chain (Table 1). For the batch experiments, two types of syngas elongation reaction towards longer carbon chain car- fermentation effluent were tested. The first effluent type boxylic acids, including n-caprylic acid [22, 23, 29]; and was obtained from the second stage of a two-stage syn- (ii) selective in-line extraction of longer chain products gas fermenter operated as described by Richter et al. [31]. results in higher product specificities [23, 30]. Currently, The influent of the syngas fermenter consisted of× 2 con- microbiome studies are achieving high production rates centrated P7 medium (Additional file 1, [32]). The second of n-caprylic acid [22], but this product has not yet been effluent type was collected from a single-stage syngas detected in pure C. kluyveri studies. fermenter operated with mineral medium, which was To address the aforementioned knowledge gaps, we adapted from Mock et al. [33] (Additional file 1). We used have conducted experiments using a pure culture of the second effluent type for our bioreactor experiments. C. kluyveri in bioreactors to investigate whether syn- The collected effluent was kept frozen− ( 20 °C) until use. gas fermentation effluent can be directly used as a Next, the effluent was filtered with a 0.2-µm vacuum fil- growth medium for C. kluyveri. We report for the first ter to obtain a sterile influent for the C. kluyveri experi- time n-caprylic acid production by a pure culture of C. ments. The concentrations of ethanol and acetic acid kluyveri. In addition, we elaborate on key challenges to were determined in the filtered substrate and ethanol was obtain high-rate MCCA production from syngas fermen- supplemented when needed to obtain the desired con- tation effluent in bioreactors with and without in-line centration (Table 1). Trace elements, vitamins, selenite– product extraction. In the context of this article “car- tungstate (as for DSMZ52 medium), and cysteine were boxylic acids” is used as the general term for the prod- added after filtration. We omitted yeast extract from the ucts obtained. Depending on the pH of the processes bioreactor experiments.

Table 1 Theoretical composition of the substrate (ethanol and acetic acid) during the operating period for the bioreactor with pertraction (BP) and without pertraction (BNP)

1 1 1 1 1 1 Day (Phase) OLR BP (g COD L− day− ; mM-C day− ) OLR BNP (g COD L− day− ; mM-C day− ) HRT (d) Ethanol/acetic acid ratio

1–18 (I) 12 (257) 12 (257) 2 10 18–28 (II) 6 (129) 6 (129) 4 10 28–37 (III) 6 (129) 10 (215) 2 10 37–48 (IV) 10 (215) 10 (215) 2 10 48–74 (V) 15 (322) 15 (322) 2 10 74–85 (VI) 15 (340) 15 (340) 2.3 3 86–95 (VII)a 15 (340) 15 (340) 2.3 3

1 Ethanol and acetic acid have a COD content of 96 and 64 g COD mol− , respectively HRT hydraulic residence time, COD chemical oxygen demand, OLR organic loading rate a Real syngas fermentation effluent was used Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 4 of 15

Batch‑growth experiment with syngas fermentation inoculum, and transferred in each specific medium effluent for two growth cycles to dilute the original DSMZ52 Growth and production of C. kluyveri were tested in medium and to allow adaptation of the culture. A trip- eight different media with and without additions of vari- licate bottle test was subsequently carried out. Incuba- ous chemicals to evaluate the use of syngas fermentation tion (without shaking) of the triplicate bottle test took effluent as growth medium for a C. kluyveri bioreactor place at 30 °C, which was the same temperature used (Table 2). The eight different media used in the batch for bioreactor operation. The pH of the media was not test were as follows: (i) DSMZ52 C. kluyveri medium controlled during the experiment (Additional file 2). (DSMZ); (ii) P7 syngas fermentation effluent with only Bioreactor setup for continuous experiments bicarbonate added (SGP−); (iii) P7 syngas fermentation effluent with trace elements, vitamins, selenite–tung- Two BioFlo310 Benchtop fermenters (New Brunswick state, and bicarbonate added (SGPT−); (iv) P7 syngas Scientific Co, CT, USA), with a 2.5-L vessel (operating fermentation effluent with trace elements, vitamins, sel- volume of 1.5 L), were used for the bioreactor experi- enite–tungstate, and bicarbonate, as well as yeast extract ments. The headplate of each bioreactor was equipped added (SGPT+); (v) Mock syngas fermentation effluent with a sampling port; gas sparger; exhaust condenser; with only bicarbonate added (SGM−); (vi) Mock syn- mixing system (200 rpm); a pH probe (Mettler Toledo gas fermentation effluent with trace elements, vitamins, 405-DPAS-SC, Mettler Toledo, OH, USA); an inlet for selenite–tungstate, and bicarbonate added (SGMT−); influent, acid, and base; an outlet for both recirculation (vii) 2× concentrated P7 medium with only bicarbonate and effluent; and an inlet for the recirculated broth. The added (P−); and (viii) 2× concentrated Mock medium temperature was controlled at 30 °C using the built-in with only bicarbonate added (M−). Trace elements, vita- water jacket. Each bioreactor system included an exter- mins, and selenite–tungstate solutions were prepared nal recirculation pump (Masterflex, IL, USA). Bioreactor and added according to the DSMZ52 medium recipe broth was recirculated at 120 mL min−1 over a hollow- (Additional file 1). fiber membrane (Cell guard, Minikros Sampler, 20 cm, All media contained 1 mM cysteine as a reducing pore size 0.2 µm, PES, Spectrumlabs, CA, USA) to retain agent. The combined chemical oxygen demand (COD) all cells in the bioreactor. The cell-free medium that we from ethanol and acetic acid was the same for each obtained from the hollow-fiber unit was pumped out −1 medium. The 2× P7 medium was prepared using the as effluent at a rate of 750 mL day . The same volume mineral solution of the P7 medium, with additions of influent medium was pumped in daily, resulting in according to the DSMZ52 medium and the COD and an HRT of ~2 days. The bioreactors were continuously ethanol/acetic acid ratio of the DSMZ52 medium. sparged with anaerobic gas, consisting of 20 mL min−1 −1 −1 The 2× Mock medium was prepared with only etha- N2 and 5 mL min CO2, at a flow rate of ~25 mL min . nol and acetic acid added before the transfer of C. The flow rates of the two gases were manually controlled kluyveri (Additional file 1). The experiment was car- using flow meters (65-mm Correlated Flowmeter with ried out in three separate batches, each time with the valve, aluminum, Cole-Parmer, IL, USA). Both bioreac- DSMZ52 medium as the control. An active C. kluyveri tors were initially controlled at pH 7, using 2 M KOH and culture growing in DSMZ52 medium was used as 2 M HCl.

Table 2 Composition of the media tested in the batch-growth experiments Condition Ethanol (mM) Acetic acid (mM) Vitamins Trace elements Selenite–tungstate Yeast extract Bicarbonate

DSMZ 343 101 Y Y Y Y Y SGP 315 144 N N N N Y − SGPT 315 144 Y Y Y N Y − SGPT 315 144 Y Y Y Y Y + SGM 343 101 N N N N Y − SGMT- 343 101 Y Y Y N Y P 343 101 Y Y Y N Y − M 343 101 Na Na Na N Y − The test was carried out as three separate experiments, each time with DSMZ52 medium (DSMZ) as the control. Each medium contained the same COD concentration. Additions were made based on the DSMZ52 medium. Ethanol and acetic acid concentrations depicted here are the theoretical concentration N not added, Y added a The vitamins and trace elements for the 2 Mock medium were used × Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 5 of 15

Pertraction system Bioreactor startup and operation One of the two bioreactors was equipped with a mem- The bioreactors were filled with medium, autoclaved, and −1 brane-based liquid–liquid extraction system (pertrac- sparged with sterile N2/CO2 at a flow rate of 25 mL min tion), consisting of a forward and backward extraction for 24 h. Liquid samples were taken before inoculation. module (Fig. 2). We refer to this bioreactor as the bio- Each bioreactor was inoculated at a 7.5% (v/v) concen- reactor with pertraction (BP). The other bioreactor was tration using serum flask-cultures of C. kluyveri. In the referred to as the bioreactor with no pertraction (BNP). bioreactor experiments described next, continuous mode The pertraction system was connected and started on was started after 12 h in batch mode, at an OLR of 12 g day 11 of the bioreactor experiment. This system extracts COD L−1 day−1. In initial runs, continuous-mode opera- carboxylic acids into a solvent, based on their hydro- tion was started when the optical density (OD) was above phobicity, and subsequently into an alkaline stripping 1, or, in a later run this was done as soon as the OD was solution, based on a pH gradient between the bioreac- higher than 0.3. The OLR applied upon transitioning to tor and the stripping solution [18]. The cell-free filtrate continuous mode was 2 g COD L−1 day−1 in the initial leaving the hollow-fiber unit (cell guard) was pumped at runs, and was later increased to 8 g COD L−1 day−1. The 90 mL min−1 into the shell side of the forward extrac- faster transition and increased OLR were chosen because tion module (2.5 × 8 Liqui-Cel Membrane Contactor, the culture had shown sporulation behavior (visual obser- Membrana, Germany). There it contacted the hydro- vation with a phase-contrast microscope, Nikon Labo- phobic solvent, which consisted of mineral oil contain- phot, Nikon, NY, USA). The operating period consisted ing 30 g L−1 tri-n-octylphosphine oxide (TOPO; Sigma of seven different operating phases, which were separated Aldrich, MO, USA). The mineral oil was recirculated based on the OLR, the ethanol/acetic acid ratio, or the on the tube side between the two extraction modules at synthetic vs. real syngas fermentation effluent (Table 1). a flow rate of 7.5 mL −min 1. In the backward module, After two initial phases during which the flow rate was the mineral oil contacted the stripping solution, which halved (Phase I and II), the OLR was gradually increased was recirculated at 75 mL min−1. The stripping solution during the remaining operating period (Phases III–VII). consisted of 300 mM Na2B4O7, which was controlled Liquid samples were taken at least four times per week. at pH 9.0 using 5 M NaOH. The stripping solution was Gas flow rate and composition, effluent volume, and vol- regularly refreshed to keep the total carboxylate concen- ume of dosed acid and base were also measured during tration below 120 mM. We calculated the product forma- sampling. Possible losses of ethanol or carboxylic acids tion from the accumulation of product in the stripping via the exhaust gas were not quantified, although these solution between two sampling times and the volumetric could have taken place despite the use of an exhaust con- production rate based on reactor broth concentrations denser [34]. In the figures and tables, we show most of and hydraulic residence time. the results as mM product. Specificities were calculated

Fig. 2 Bioreactor setup for fermentation with in-line product extraction (pertraction). The bioreactor broth is sent through a hollow-fiber unit (cell guard) to obtain a cell-free effluent and broth for the pertraction system Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 6 of 15

as weighted averages of the ratio of the carbon (mM- Shimadzu LabSolutions data analysis software was used C) in the product of interest and the carbon (mM-C) in to integrate ethanol and acetic acid peaks. Concentra- n-butyric acid, n-caproic acid, and n-caprylic acid com- tions of carboxylic acids (C4–C8) were measured using bined, which were measured during at least three time a gas chromatograph (HP5890, Hewlett Packard, USA), points during steady state. Carbon conversion efficiencies which was equipped with a 7683 auto-injector and flame were calculated as weighted averages based on the input ionization detector. Columns [capillary GC column carbon (mM-C ethanol and acetic acid) and the carbon (Nukol); 15 m × 0.53 mm internal diameter (Supelco)] for products in both the effluent and extraction solution were purchased from Sigma Aldrich, Inc. (USA). The (mM-C butyric acid, n-caproic acid, and n-caprylic acid), flow rates of hydrogen, air, and helium were 21.4, 350, which were measured during at least three time points and 35 mL min−1, respectively. The temperature was first during steady state. set to 70 °C for 2 min, and then ramped up to a final tem- Four technical problems decreased the efficiency of the perature of 200 °C at 12 °C min−1, where the temperature pertraction system at certain time points: (i) mineral oil was held for 2 min. The injection port temperature and leakages took place on day 20 and 38; (ii) the actual min- detector temperature were 200 and 275 °C, respectively. eral oil recirculation rate was lower than the set-point from day 30 to 76; (iii) bioreactor broth was lost due to Microbiome analysis a tubing breakage in the pump line on day 87 (first inci- Biomass samples were collected from both BP and BNP dent) and 95 (second incident); and (iv) a short circuit at two time points: day 37 and 45. Approximately 2 mL of in the broth flow was identified and remedied on day bioreactor broth was centrifuged at 13,000 rpm (Eppen- 89. Due to this short circuit, bioreactor broth contain- dorf Centrifuge 5415D, Eppendorf, Hauppauge, NY, ing biomass was siphoned into the cell-free broth feed- USA) and the supernatant was discarded. Samples were ing the effluent line. Both bioreactors were discontinued stored at −20 °C until further processing. Genomic DNA after the second incident involving bioreactor broth loss was extracted from bioreactor samples using the MO on day 95. BIO PowerSoil kit (MO BIO Laboratories Inc., Carlsbad, CA, USA). Modifications to the manufacturer’s proto- Analytical procedures col were described previously [35]. In brief, custom bead The OD was measured at 600 nm using a spectropho- tubes with 0.1-mm and 0.5-mm diameter silica/zirconia tometer (Spectronic 1201, Milton Roy, NJ, USA; quartz beads were assembled in a sterile laminar flow hood. Cell cuvette, Starna Cells, CA, USA). Phosphate buffer lysis for DNA isolation was performed by bead-beat- (50 mM, pH 6.8) was used to dilute the samples, if nec- ing at 3550 oscillations per min for 45 s. To profile the essary. For the batch experiment, 200 µL broth was microbial community within each sample, DNA samples analyzed using a 96-well plate in a plate reader (BioTek were amplified for the V4 region of the 16S rRNA gene. Synergy 4, BioTek, VT, USA). The reading of the pH The PCR amplification protocol was described previ- probes in the bioreactors was controlled at least four ously [35]. Purified PCR amplicons were pooled to 4 ng times per week by measuring the pH with an external pH per sample, and submitted for Illumina MiSeq sequenc- probe, calibrated using buffers at pH 4, 7, and 10 (Orion ing (Cornell Genomics Facility, Cornell University Insti- Star A329, Thermo Fischer Scientific, MA, USA). tute of Biotechnology, Ithaca, NY). We used QIITA Gas samples were analyzed on a gas chromatograph (qiita.microbio.me) to quality filter and demultiplex raw (GOW-MAC Instrument Co., PA, USA), which was sequences. Sequences were separated into groups (or equipped with a column (1.8 m; 80/100 Hayesep Q pack- operational taxonomic units, OTUs) of similar sequences ing material; Supelco, PA, USA) at 25 °C, using helium as (97% similarity) using the sortmerna method. OTUs were the carrier gas. The ratio of the integrated peak areas for referenced against the Greengenes v13.8 database [36]. N2 and CO2 was determined using PeakSimple software Singletons (rare OTUs) were removed to filter out OTUs v4.44 (Schemback, Germany). Ethanol and acetic acid with one count across all samples. Bacterial abundance concentrations were determined using a HPLC system profile was calculated in MacQIIME v1.9.1 [37]. (Shimadzu Prominence HPLC system, Columbia, MD, USA), which was equipped with the following compo- Results and discussion nents: the SIL-20AC HT autosampler, RID-10A refrac- Trace elements and/or vitamins must be added to syngas tive index detector, CTO-20AC column oven, and the fermentation effluent to grow C. kluyveri CBM-20A communications bus module. Compounds Yeast extract is often added to enhance growth and pro- were separated in an Aminex HPX-87H analytical col- duction rates of C. kluyveri although it is known that it umn at 65 °C (Bio-Rad, CA, USA), using sulfuric acid can be substituted by biotin and p-aminobenzoic acid (5 mM, flow rate 0.6 mL min−1) as the mobile phase. The [38, 39]. Both batch-growth experiments with (1) original Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 7 of 15

DSMZ52 medium (DSMZ) with yeast extract and (2) A1). In all the fermentation broth solutions of the batch- Mock syngas fermentation effluent with trace elements, growth experiments, the pH values remained above 6 vitamins, and selenite–tungstate added, but without yeast (Additional file 2). From these results, we concluded that extract (SGMT−) showed the fastest growth, highest OD, the addition of undefined yeast extract is not necessary to and highest concentration of n-caproic acid produced sustain growth of C. kluyveri when coupling syngas fer- after 2 weeks (Fig. 3 A1–B3). In addition, P7 syngas fermentation and chain elongation. However, the use of raw mentation effluent-based medium with additional trace syngas fermentation effluent is also not possible because elements, vitamins, and selenite–tungstate, but without growth in this condition was retarded for the P7-based yeast extract (SGPT−), resulted in shorter lag phase than effluent (SGP−) (Fig. 3 A1, B1). Certain trace elements the same medium with yeast extract (SGPT+) (Fig. 3 or vitamins are missing in the raw syngas fermentation

Fig. 3 Three separate batch experiments (1, 2, and 3) were carried out. a Growth (as OD) was highest for the standard DSMZ52 (DMSZ) medium and the Mock medium syngas fermentation effluent with added growth factors, but no yeast extract. b Production of n-caproic acid was the highest in the standard DSMZ52 medium, but comparable results were obtained with syngas fermentation effluent with additions. Data represent the mean (n 3), error bars indicate the standard deviation = Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 8 of 15

effluent. This effluent contains cell material from dead sulfur source. We postulated that this would not affectC. cells or excretion products from living cells during syngas kluyveri because they are endowed with cysteine degra- fermentation and the unused trace elements, vitamins, dation genes [44]. As anticipated, growth of the culture and nutrients that were added to the original substrate of was not affected by the change from sulfate to cysteine the syngas fermentation system. Yeast extract is typically as the sulfur source. SRB contamination was successfully not added to syngas fermentation with the goal to boost avoided in the subsequent bioreactor runs. the production of ethanol, and therefore some trace ele- Second, we visually observed sporulation of the culture ment and/or vitamin is likely missing. Before developing with a phase-contrast microscope (Additional file 4). We an industrial-scale system, syngas fermentation efflu- hypothesized that sporulation was triggered by a lack of ent should be fully characterized. An economic analy- carbon source or nutrients at the end of the exponential sis is then needed to ascertain whether the introduction growth phase during the batch-wise startup or just after of certain trace elements or vitamins vs. the addition of the switch to the continuous-mode operation [45]. How- yeast extract is more economically attractive [40]. ever, a faster transition to continuous mode or higher loading rates did not avoid sporulation. The use of the Clostridium kluyveri can produce n‑caprylic acid (C8) hollow-fiber unit to retain cells in the bioreactor makes In seven out of eight medium conditions during the the startup in batch mode unnecessary for our contin- batch-growth experiments (all except P−), n-caprylic acid uous-mode operation. Therefore, the bioreactors were was detected, with the highest concentrations occurring subsequently started in continuous mode directly at a −1 −1 with Mock syngas fermentation effluent (2.19 ± 0.34 mM loading rate of 12 g COD L day . However, using this after 14 days) (Additional file 3). n-Caprylic acid pro- operating strategy, the culture still sporulated. In fact, duction has been reported for reactor microbiomes, sporulation was initiated even faster compared to batch- including those with a high abundance of C. kluyveri mode operation (day 3 instead of day 5). Fortunately, [18, 27, 41]. However, this is the first time that produc- the spores also germinated again within 2 days, forming tion of n-caprylic acid is reported for a pure culture of C. thinner C. kluyveri cells compared to the cells from the kluyveri. Chain elongation takes place through the reverse initial culture (Additional file 4). The culture regained its β-oxidation pathway, which is a cyclic process (Fig. 1). In original appearance during the operating period, lead- the first step, two acetyl-CoA molecules are combined to ing to successful runs. Since we stopped the earlier runs form butyryl-CoA, which may be reduced to n-butyric immediately after we had observed sporulation, we do acid. Alternatively, butyryl-CoA may enter a second not know whether germination would or would not have round of chain elongation where it is coupled to another occurred then. The sporulation and germination behav- acetyl-CoA forming hexanoyl-CoA, which may then be ior of C. kluyveri should be further studied in detail to reduced to n-caproic acid. Most likely, C. kluyveri has understand the mechanisms, and possible impacts on the capacity to produce n-caprylic acid through a similar long-term reactor operation. cycle, coupling acetyl-CoA to hexanoyl-CoA under more Both BP and BNP showed similar behavior in the reduced conditions [27, 42]. Carboxylic acids generally 10 days after startup in continuous mode and before the become more toxic with increasing chain length. This tox- pertraction was initiated for BP (Fig. 4). During Phase I of icity is a possible explanation for the absence of n-caprylic the operating period, the optical density increased within acid detection in previous studies. The other explanation 3 days, dropped when sporulation occurred (Additional is that n-caprylic acid was simply not analyzed. file 4), and increased again when the cells germinated (Additional file 5). Production of n-butyric acid and Continuous‑mode operation with C. kluyveri requires a n-caproic acid followed the growth pattern, resulting in specific startup procedure an n-caproic acid concentration of 33 mM for BP and Initial attempts to start the bioreactors with synthetic 31 mM for BNP on day 3 after which a drop in produc- medium were not successful due to two key reasons: (1) tion occurred due to sporulation between day 3 and 6 contamination; and (2) sporulation. First, sulfate-reduc- (Additional file 6). The production for BNP then followed ing bacteria (SRB) contaminated the culture despite our a cyclic pattern, with either peaking substrate concentra- axenic culturing methods, resulting in an H2S-like odor. tions (ethanol and acetic acid in Additional files 6, 7) or The SRB reduce sulfate, using 2H or acetic acid as elec- product concentrations (n-butyric and n-caproic acid in tron donor [43]. Hydrogen gas is produced by C. kluyveri Additional file 6). Metabolic oscillations coupled to spor- during chain elongation, while acetic acid (electron ulation have been previously reported for solventogenic acceptor) and sulfate (sulfur source) are components of Clostridia due to a periodic shift between acidogenic the DSMZ52 medium used for this study. To prevent (primary) and solventogenic (secondary) metabolisms contamination, sulfate was replaced by cysteine as the [46–49]. The cyclic behavior disappeared when the Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 9 of 15

Fig. 4 Production rates of n-butyric acid (gray dotted line), n-caproic acid (gray line), and n-caprylic acid (black line) during continuous-mode operation of the bioreactor with pertraction (BP, top, operating pH 6) and without pertraction (BNP, bottom, operating pH 7). The moving average (n 7) = for the n-caproic acid concentration is provided. The seven operating phases (Table 2) are marked with vertical lines

loading rate was decreased to 6 g COD L−1 day−1 on day were always higher (Table 3). In a continuous mode and 17 during Phase II (Fig. 4). with a completely mixed system, the ethanol concentra- Pure-culture fermentations are often executed in tion will be low due to substrate removal when the sys- batch-mode operation rather than in continuous-mode tem is not overfed, which prevents ethanol inhibition operation. Our results suggest that continuous-mode [23]. In addition, the continuous removal of product with operation would be more advantageous. The batch- the effluent will reduce the accumulation of MCCAs, cir- growth experiment and Phase VI of the operating period cumventing the product inhibition that is anticipated at for the continuous-mode operation can be compared the end of the operating period of a batch-mode opera- because similar ratios of ethanol and acetic acid were tion. The faster sporulation behavior of our culture dur- used (3:1). In the continuous mode, the n-caproic acid ing continuous-mode operation did not negatively affect production rates, specificities, and conversion efficiencies process outcomes in the long term. Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 10 of 15 101 ± 2.7 94.4 ± 6.6 65.0 ± 26.5 77.0 ± 4.5 100.0 ± 0.0 Extr. C8 (%) Extr. 64.8 ± 13.7 37.8 ± 27.2 80.4 ± 10.5 42.7 ± 6.9 Extr. C6 (%) Extr. 70.0 ± 40

41.9 ± 2.5 38.5 ± 12.6 38.9 ± 17.4 90.1 ± 0.7 79.9 ± 2.0 93.6 ± 4.4 Carbon conversion conversion Carbon efficiency (%) 54.7 ± 6.5 47.5 ± 2.5 65.9 ± 17.4 76.4 ± 19.5 3.9 ± 2.2 6.4 ± 3.0 3.7 ± 2.9 6.7 ± 0.7 4.0 ± 0.4 7.4 ± 0.3 8.5 ± 0.4 8.1 ± 0.2 1.9 ± 1.6 Specificity C8 (%) 10.8 ± 1.2

90.9 ± 2.0 87.7 ± 3.9 88.5 ± 10.1 84.2 ± 1.0 Specificity C6 (%) 83.0 ± 1.0 81.4 ± 0.5 84.7 ± 1.5 85.5 ± 1.2 86.5 ± 0.5 79.5 ± 1.9 ) − 1 0.6 ± 0.4 1.0 ± 0.4 0.2 ± 0.1 1.4 ± 0.2 2.6 ± 0.01 1.8 ± 0.3 1.2 ± 0.1 0.8 ± 0.2 n -Caprylic acid (mM day 2.14 ± 0.4 0.47 ± 0.3 ) − 1 8.4 ± -Caproic acid n -Caproic (mM day 16.2 ± 5.4 19.1 ± 6.6 35.3 ± 2.7 39.9 ± 0.9 37.6 ± 1.6 18.6 ± 2.9 15.7 ± 0.5 11.1 ± 2.7 23.1 ± 4.7 ) − 1 n -Butyric acid (mM day 1.3 ± 0.2 1.7 ± 0.4 0.9 ± 0.7 5.7 ± 0.7 9.4 ± 0.7 7.8 ± 0.7 1.5 ± 0.2 1.7 ± 0.3 1.0 ± 0.3 7.8 ± 0.11 ) − 1 OLR (mM-C day 255.2 ± 7.4 298.3 ± 9.6 151.9 ± 31.4 279.7 ± 27 370.0 ± 9.7 296.5 ± 0.7 241.0 ± 28.4 233.0 ± 7.9 122.5 ± 31.7 244.6 ± 74.4 ) − 1 day − 1 10.9 ± 0.4 14.2 ± 1.0 7.0 ± 0.4 12.3 ± 1.2 16.3 ± 0.4 13.0 ± 0.03 11.3 ± 1.2 10.9 ± 0.4 6.9 ± 0.2 10.7 ± 3.3 OLR (g COD L Overview of critical for the performance parameters bioreactor with pertraction pH 6) and the (BP; bioreactor without pertraction pH 7) for the (BNP; V VII VI VI V III–IV II VII IV II–III Phase 3 -caproic acid, C8 n -caprylic C6 n -caproic extraction acid, demand, chemical oxygen efficiency Extr. acid, BP BNP Table COD n ≥ 3 and for after a change in condition), periods (starting state the steady 3 HRTs taken for were averages products ( n -butyric,Weighted n -caproic the three and n -caprylic for rates shown. Production acid) are ± stdev) 1 (average phases as defined in Table operating different Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 11 of 15

The mildly acidic pH value of 5.5 was not favorable for C. concentration of undissociated acids at the membrane kluyveri boundary [52]. At a loading rate of 10 g COD L−1 day−1 The pH for BP was decreased from 7.0 to 5.5 in one step (Phase IV), the average efficiency forn -caproic acid on day 11 to immediately ensure an efficient pertrac- extraction was only 65% (Table 3). With open cultures, tion rate of the undissociated carboxylic acid products. a removal efficiency of greater than 95% for n-caproic All n-caproic acid, which was present in the bioreac- acid has been achieved with a similar pertraction system tor broth before day 11, was quickly extracted after this at mildly acidic pH values of 5.5 [53]. During Phase VI, pH decrease (Additional file 6), but the production of the concentration of undissociated n-caproic acid was MCCAs ceased as well (Fig. 4) and the OD decreased 3.5 ± 0.4 mM in BP (pH 6) due to the relatively ineffi- (Additional file 5). In early studies with C. kluyveri, the cient extraction. This is within the concentration range pH range that allowed growth was found to be between typically reported to be toxic for pure or open cultures, 6.0 and 7.5, with a pH optimum of 6.4 [26, 28]. A recent depending on the concentration of other undissociated isolate of C. kluyveri from bovine rumen, however, was carboxylic acids (0.66–7.5 mM; [50, 51, 53]). For BNP able to grow and produce n-caproic acid at a pH as low as (pH 7), the undissociated n-caproic acid concentration 4.8 [50]. In addition, a co-culture of C. autoethanogenum was 0.54 ± 0.07 mM, which is considerably lower and and C. kluyveri was functional at a pH of 5.5, albeit at a outside of the inhibiting concentration. At mildly acidic relatively low n-caproic acid production rate [51]. Open- conditions, it is, therefore, essential to operate an optimal culture bioreactors with pertraction have been operated pertraction system or other extraction technology to pre- at a pH of 5.5 without noticeable challenges, while C. vent product toxicity. kluyveri became enriched with increasing n-caproic acid production rates [18, 21]. We observed similarities and differences Bioreactor studies without extraction operate usually between extraction at a pH of 6 (BP) and without at a neutral pH and with higher dilution rates to prevent extraction at a pH of 7 (BNP) product toxicity. C. kluyveri was found to be abundant in During Phases III, IV, and V, the OLR was gradually these microbiomes [27]. The toxicity of the undissociated increased (Tables 2, 3). This increase was slower in BP MCCAs at mildly acidic conditions is one main reason following the decrease in the pH value. For BP, the OLR for the growth inhibition of C. kluyveri (and other bac- of 10 g COD L−1 day−1 resulted in n-caproic acid pro- −1 −1 −1 teria) in microbiomes [18, 27]. However, here we found duction rates of 16.2 ± 5.4 mM day (1.9 g L day ; that the other main reason is the pH value of 5.5 directly 4.2 g COD L−1 day−1). For BNP, n-caproic acid was −1 as the inhibitor for the growth of C. kluyveri, because all produced at a similar rate of 15.7 ± 0.5 mM day MCCAs were extracted from the broth. In future experi- (1.8 g L−1 day−1; 4.0 g COD L−1 day−1) (Fig. 4). These ments, a more gradual pH decrease from 7 to 5.5 should production rates with C. kluyveri are not only com- be tested as an operating strategy. Alternatively, a newly parable for these two bioreactors but also for open- isolated and acid-tolerant chain-elongating strain, or the culture bioprocessing systems at similar OLRs with acid-tolerant C. kluyveri strain as described by Weimer a complex substrate and extraction [53]. On day 48 et al. [50], could be considered as a more ideal biocatalyst of the operating period (Phase V), we increased the for pure-culture bioprocessing. To restart production in OLR to 15 g COD L−1 day−1; however, after meas- BP, we increased the pH from 5.5 to 6.0 on day 20 of the urement, the actual loading rates were found to operating period after which additional inoculum was be slightly lower (14.2 and 13.0 g COD L−1 day−1; spiked into the bioreactor. Production of n-caproic acid Table 3). n-Caproic acid production rates dur- resumed, but during Phase II the production rates and ing the steady state period at this loading rate (days −1 −1 −1 carbon conversion efficiencies remained lower for BP at a 55–74) were 19.1 ± 6.6 mM day (2.21 g L day ; −1 −1 −1 pH of 6 than for BNP at a pH of 7 (Additional file 8). 4.9 g COD L day ) and 18.6 ± 2.9 mM day (2.16 g L−1 day−1; 4.8 g COD L−1 day−1) for the BP and Pertraction at a pH of 6 was not optimal BNP, respectively (Table 3). The production rates were, The efficiency of the pertraction system in BP was antici- thus, similar for these bioreactors. pated to be considerably lower at a pH value of 6.0 com- n-Caproic acid was the main product at an OLR of pared to 5.5. At a pH of 6.0, only 6.6% of the n-caproic 10 g COD L−1 day−1 during Phase IV with a specificity of acid is present in the undissociated form, while this is 90.9 ± 2.0 and 85.5 ± 1.2% in their products for BP and 18.3% at a pH of 5.5. Because the undissociated acids are BNP, respectively (Table 3). The other products of chain transferring from the fermentation broth into the min- elongation were n-butyric and n-caprylic acid. n-Caprylic eral oil through the membrane of the forward module, acid specificity was limited to 3.9 ± 2.2% for BP and the pertraction rates were positively correlated to the 8.5 ± 0.4% for BNP (Table 3). Although n-caprylic acid Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 12 of 15

is preferentially extracted from BP via pertraction com- for n-caproic acid remained relatively stable, however, pared to n-caproate, we observed a higher n-caprylic acid because proportionally more n-butyric acid was produced production rate without extraction at a pH of 7 (BNP). rather than n-caprylic acid. The lower specificity was We postulate that the higher pH value of 7 compared to anticipated as early work already found that a high etha- 6 reduced the toxicity for undissociated n-caprylic acid nol/acetic acid ratio is beneficial to obtain longer chain enough to explain the higher n-caprylic acid specifici- products [29]. Second, the carbon conversion efficiency ties, but more research is necessary to substantiate this increased with lower ethanol/acetic acid ratios (Table 3). claim. More research is also required to understand the The increase in efficiency can be partly explained for long-term effect of n-caprylic acid production on the cul- BNP due to the complete consumption of ethanol after ture, as well as how metabolism can be steered toward the ratio decrease (Additional file 7). In addition, for BP this product. Kucek et al. [22] did achieve a much higher and BNP, the production rates of all three carboxylic n-caprylic acid specificity at a mildly acidic pH value with acids increased with an increase in n-caproic acid pro- −1 −1 −1 a microbiome that was supplied with a similar synthetic duction rates to 39.9 ± 0.9 mM day (4.6 g L day ; −1 −1 −1 syngas fermentation effluent with an ethanol/acetic acid 10.2 g COD L day ) and 37.6 ± 1.6 mM day ratio of 10:1 (molar basis) similar to our study. However, (4.4 g L−1 day−1; 9.7 g COD L−1 day−1), respectively. their microbiota did not contain C. kluyveri as a domi- At this point, we can only speculate about why this nant bacterium. occurred. When the consumed ethanol/acetic acid ratio Sequencing revealed a certain degree of contamination is higher, more ATP is produced, and as a result more in the bioreactors (Additional file 9). The contamination biomass is grown in the bioreactor [23, 29, 56]. Within did not affect bioreactor functionality because promis- the reverse β oxidation pathway, ATP is formed via both ing conversion rates were obtained for both bioreactors. substrate-level phosphorylation and transport-coupled Other pure culture processes, such as yeast ethanol fer- phosphorylation [25, 42]. During a period of higher mentation and biopharmaceutical production, typically ethanol availability, the anaerobic oxidation of ethanol, encounter a certain level of contamination as well (up to which is coupled to chain elongation, would provide 5% relative abundance), which does not affect the pro- more energy through substrate-level phosphorylation. duction process [54]. Contamination was higher in BP Lowering the ethanol/acetic acid ratio would shift more (Additional file 9), which could be due to: (i) the inabil- ATP production toward transport-level phosphoryla- ity to sterilize the extraction modules prior to use; (ii) an tion. We speculate that chain elongation becomes more accident that could have contaminated the substrate bot- efficient as a result due to lower biomass production. The tle on day 43; and (iii) the occurrence of a short circuit higher substrate conversion efficiency may then have in the system, rendering the bioreactor vessel in contact been a mechanism to compensate for the decreased ATP with the open air via the effluent line. The increase in the production [25]. However, further research, including complexity from adding product extraction rendered the thermodynamic and metabolic modeling, is needed to system more prone to contamination. The majority of substantiate this hypothesis. the contaminants belonged to an unknown family in the order Burkholderiales (Additional file 9). The 16S rRNA Chain elongation can be coupled to syngas fermentation gene from this microbe is 100% identical compared to a with a pure culture microbe that was found within a natural biofilm on stain- Real syngas fermentation effluent was used as the less steel and PVC [55]. In BP, the relative abundance of substrate for both bioreactors starting on day 86 C. kluyveri increased while the abundance of contami- (Phase VII). n-Caproic acid was produced at a −1 −1 −1 nants decreased from day 37 to 45. This indicates com- rate of 35.3 ± 2.7 mM day (4.1 g L day ; 9.0 g munity resilience, and that events causing contamination COD L−1 day−1) for BNP, corresponding to a specific- did not lead to dominance of contaminating species dur- ity of 84.2 ± 1.0% (Table 3). Influent carbon was con- ing the operating period of our study. verted to products (n-butyric acid, n-caproic acid, and n-caprylic acid) at an efficiency of 90.1 ± 0.7% (Table 3). The carbon efficiency increased when we lowered the We did not observe a decrease in production rate or con- ethanol/acetic acid ratio version efficiency when we switched from synthetic to During Phase VI, the ethanol/acetic acid ratio in the syn- real syngas fermentation effluent (without yeast extract, thetic feed was decreased from 10:1 to 3:1 to match the but with trace elements, vitamins, selenite–tungstate, ratio in the real syngas fermentation effluent that was and cysteine). Therefore, a two-step process for the con- available. This resulted in two changes. First, the speci- version of syngas fermentation effluent to MCCAs was ficity for n-caprylic acid decreased (Table 3), which is successfully implemented. No conclusions can be drawn similar to the results by Kucek et al. [22]. The specificity for BP, because steady state had not been achieved when Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 13 of 15

the experiment was terminated on day 95 due to an well as the influence of product extraction with an opti- accident. mized design at high loading rates. Diender et al. and Richter et al. have recently shown Additional files that a direct conversion of syngas to n-caproic acid with a co-culture of a carboxydotrophic bacterium and C. Additional file 1. Media used for syngas fermentation; Media kluyveri is also possible [51, 57]. However, they found compositions. that a pH discrepancy exists between the two mem- Additional file 2. Batch growth experiment: pH profile; Figure S1 with bers in the co-culture, and that n-caproic acid was fur- heading and explanation. ther reduced to n-hexanol, resulting in a low specificity Additional file 3. n-Caprylic acid concentrations during batch experi- for either product. Therefore, a two-stage system would ments; Table S1 with heading and explanation. allow better control of process conditions by providing Additional file 4. Visual observation of the sporulation behavior of C. different pH values and temperatures for the two bio- kluyveri; Figure S2 with heading and explanation. processes. In addition, the syngas fermentation in the Additional file 5. Optical density; Figure S3 with heading and first stage can be operated specifically to achieve the opti- explanation. mum ethanol/acetic acid ratio for further chain elonga- Additional file 6. Word document (.docx); Concentrations of carboxylic acids in the bioreactor broth; Figure S4 and S5 with headings and tion in the second stage. It should also be noted that the explanations. first stage (syngas fermentation) has already undergone Additional file 7. Ethanol concentrations in the bioreactors; Figure S6 considerable optimization and that full-scale plants are with heading and explanation. being built. From a practical point of view, it may be eas- Additional file 8. Conversion efficiency; Figure S7 with heading and ier to build another stage for chain elongation after the explanation. existing syngas fermentation stage. Additional file 9. Sequencing data; Figure S8 with heading and explanation. Conclusions This is the first long-term continuous bioreactor study Abbreviations using a pure culture of C. kluyveri as the biocatalyst for COD: chemical oxygen demand; MCCA: medium-chain carboxylic acid; OD: chain elongation. We observed n-caprylic acid produc- optical density at 600 nm; OLR: organic loading rate; SCCA: short-chain car- tion by C. kluyveri for the first time. Coupling the syngas boxylic acid; SRB: sulfate-reducing bacteria. platform and carboxylate platform was feasible without Authors’ contributions the addition of yeast extract, and instead with the addi- SG designed and executed experiments, performed analysis, interpreted data, tion of trace elements and vitamins. We observed spor- and drafted the manuscript. BM and JGU executed experiments, performed analysis, and contributed to data interpretation. MN executed and interpreted ulation events of the C. kluyveri culture during startup the microbial community analysis. KR and LTA conceived the study and partici- periods, but these events did not appear to negatively pated in its design. LTA coordinated the study and contributed to the drafting affect the long-term operating conditions. When in-line of the manuscript. All authors read and approved the final manuscript. n-caproic acid extraction via pertraction is desired, the Author details mildly acidic condition (pH of 5.5), which is necessary 1 Cornell University, Biological and Environmental Engineering, Riley‑Robb for an efficient pertraction system, inhibited C. kluyveri Hall, Ithaca, NY 14853, USA. 2 Ghent University, Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000 Ghent, Belgium. 3 University directly and not only via the increased toxicity of the of Tübingen, Center for Applied GeoSciences, Hölderlinstr. 12, 72074 Tübingen, undissociated n-caproic acid or undissociated n-caprylic Germany. 4 Present Address: Organic Waste SystemsDok Noord 5, 9000 Ghent, acid. Therefore, a different chain-elongating bacterium Belgium. with a lower pH optimum than 6–7 should be isolated. Acknowledgements Obtaining a high-rate chain elongation process will be The authors thank Tim Lacoere for drawing the bioreactor scheme. The input crucial for a successful coupling of syngas fermentation of Ramon Ganigué on the manuscript draft was greatly appreciated. and chain elongation. If methanogenesis and other com- Competing interests peting pathways can successfully be inhibited in open The authors declare that they have no competing interests. culture fermentations, this fermentation strategy would Availability of data and materials be more advantageous than a pure culture process due to The datasets generated during and/or analyzed during the current study are the simplification of the bioprocess without the require- available from the corresponding author on reasonable request. Sequence ment for axenic conditions. The study presented here data (with metadata) are available online on QIITA (http://qiita.microbio.me) with the study ID 10582. Sequences are available on the EBI GenBank data- was, however, a first proof-of-concept that a pure culture base (Accession Number: ERP020050). of C. kluyveri can act as the catalyst in this bioprocess. Follow-up studies should focus on the influence of pH on Funding This work was supported by the NSF SusChEM Program (Award# 1336186) the metabolism of C. kluyveri in continuous processes or to LTA. SG was supported by the Special Research Fund (BOF) from Ghent the selection of a different acid-tolerant biocatalyst, as University, while the research stay of SG at Cornell University was financed Gildemyn et al. Biotechnol Biofuels (2017) 10:83 Page 14 of 15

with a travel grant from the FWO (Research Foundation–Flanders) and 19. Grootscholten TIM, Steinbusch KJJ, Hamelers HVM, Buisman CJN. Chain supported with a donation from ArcelorMittal (Ghent, Belgium) to KR. BM is elongation of acetate and ethanol in an upflow anaerobic filter for high funded through a postdoctoral research fellowship from the German Research rate MCFA production. Bioresour Technol. 2013;135:440–5. Foundation (DFG, MO2933/1-1). JGU was funded through a graduate teaching 20. Grootscholten TIM, Steinbusch KJJ, Hamelers HVM, Buisman CJN. assistantship provided by the Department of Biological and Environmen- Improving medium chain fatty acid productivity using chain elongation tal Engineering at Cornell University, Ithaca, NY. KR was supported by the by reducing the hydraulic retention time in an upflow anaerobic filter. ERC Starting Grant ELECTROTALK. We acknowledge support by Deutsche Bioresour Technol. 2013;136:735–8. 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