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Chemical Engineering Journal

Elsevier BV

All preprints, ranked by how well they match Chemical Engineering Journal's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Performance effects from different shutdown methods of three electrode materials for the power-to-gas application with electromethanogenesis

Rohbohm, N.; Lang, M.; Erben, J.; Gemeinhardt, K.; Patel, N.; Ilic, I. K.; Hafenbradl, D.; Rodrigo Quejigo, J.; Angenent, L. T.

2024-05-27 bioengineering 10.1101/2024.05.22.595300 medRxiv
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Industrial applications of microbial electrochemical systems will require regular maintenance shutdowns, involving inspections and component replacements to extend the lifespan of the system. Here, we examined the impact of such shutdowns on the performance of three electrode materials (i.e., platinized titanium, graphite, and nickel) as cathodes in a microbial electrochemical system that would be used for electromethanogenesis in power-to-gas applications. We focused on methane (CH4) production from hydrogen (H2) and carbon dioxide (CO2) using Methanothermobacter thermautotrophicus. We showed that the platinized titanium cathode resulted in high volumetric CH4 production rates and Coulombic efficiencies. Using a graphite cathode would be more cost-effective than using the platinized titanium cathode in microbial electrochemical systems but showed an inferior performance. The microbial electrochemical system with the nickel cathode showed improvements compared to the graphite cathode. Additionally, this system with a nickel cathode demonstrated the fastest recovery during a shutdown experiment compared to the other two cathodes. Fluctuations in pH and nickel concentrations in the catholyte during power interruptions affected CH4 production recovery in the system with the nickel cathode. This research enhances understanding of the integration of biological and electrochemical processes in microbial electrochemical systems, providing insights into electrode selection and operating strategies for effective and sustainable CH4 production.

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Microbial Electrosynthesis from CO2 reaches Productivity of 1 Syngas and Chain Elongation Fermentations

Cabau-Peinado, O.; Winkelhorst, M.; Stroek, R.; de Kat Angelino, R.; Straathof, A.; Masania, K.; Daran, J.-M. G.; Jourdin, L.

2024-02-08 bioengineering 10.1101/2024.02.08.579422 medRxiv
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Microbial electrosynthesis allows the electrochemical upgrading of CO2. However, higher productivities and energy efficiencies are needed to reach a viability that can make the technology transformative. Here we show how a biofilm-based microbial porous cathode in a directed flow-through electrochemical system can continuously reduce CO2 to even-chain C2-C6 carboxylic acids during 248 days. We demonstrate a 3-fold higher biofilm concentration, volumetric current density, and productivity than the state of the art, up to a new record of -35 kA m-3cathode and 69 kgC m-3cathode day-1, at 60-97% and 30-35% faradaic and energy efficiencies, respectively. Most notably, the volumetric productivity resembles those achieved in lab-scale and industrial syngas (CO-H2-CO2) fermentation and chain elongation fermentation. This work highlights key design parameters for efficient electricity-driven microbial CO2 reduction. There is need and room to improve the rates of electrode colonization and microbe-specific kinetics to scale-up the technology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/579422v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@259668org.highwire.dtl.DTLVardef@1b5adedorg.highwire.dtl.DTLVardef@ada588org.highwire.dtl.DTLVardef@4eb23a_HPS_FORMAT_FIGEXP M_FIG C_FIG

3
Carbon oxidation with sacrificial anodes to inhibit O2 evolution in membrane-less bioelectrochemical systems for microbial electrosynthesis

Rohbohm, N.; Sun, T.; Blasco-Gomez, R.; Byrne, J. M.; Kappler, A.; Angenent, L. T.

2022-08-25 bioengineering 10.1101/2022.08.23.504965 medRxiv
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Microbial electrosynthesis is an emerging biosynthesis technology that produces value-added chemicals and fuels and, at the same time, reduces the environmental carbon footprint. However, constraints, such as low current densities and high inner resistance, disfavor this technology for industrial-scale purposes. The cathode performance has been strongly improved in recent years, while the anode performance has not been given enough attention despite its importance in closing the electric circuit. For traditional water electrolysis, O2 is produced at the anode, which is toxic to the anaerobic autotrophs that engage in microbial electrosynthesis. To overcome O2 toxicity in conventional microbial electrosynthesis, the anode and the cathode chamber have been separated by an ion-exchange membrane to avoid contact between the microbes and O2. However, ion-exchange membranes increase the maintenance costs and compromise the production efficiency by introducing an additional internal resistance. Furthermore, O2 is inevitably transferred to the catholyte due to diffusion and electro-osmotic fluxes that occur within the membrane. Here, we proved the concept of integrating carbon oxidation with sacrificial anodes and microbes to simultaneously inhibit the O2 evolution reaction (OER) and circumvent membrane application, which allows microbial electrosynthesis to proceed in a single chamber. The carbon-based anodes performed carbon oxidation as the alternative reaction to the OER. This enables microbial electrosynthesis to be performed with cell voltages as low as 1.8-2.1 V at 10 A{middle dot}m-2. We utilized Methanothermobacter thermautotrophicus {Delta}H in a single-chamber Bioelectrochemical system (BES) with the best performing carbon-based anode (i.e., activated-carbon anode with soluble iron) to achieve a maximum cathode-geometric CH4 production rate of 27.3 L{middle dot}m-2{middle dot}d-1, which is equal to a volumetric methane production rate of 0.11 L{middle dot}L-1{middle dot}d-1 in our BES, at a coulombic efficiency of 99.4%. In this study, Methanothermobacter thermautotrophicus {Delta}H was majorly limited by sulfur that inhibited electromethanogenesis. However, this proof-of-concept study allows microbial electrosynthesis to be performed more energy-efficiently and can be immediately utilized for research purposes in microbial electrosynthesis.

4
Rechargeable Biomineral Induced by Sulfate Reducing Bacterium Cupidesulfovibrio sp. HK-II

Arashi, Y.; Mochihara, H.; Kubota, H.; Suzuki, K.; Chiba, Y.; Kato, Y.; Kogure, T.; Moriuchi, R.; Dohra, H.; Tashiro, Y.; Futamata, H.

2023-08-08 bioengineering 10.1101/2023.08.07.552368 medRxiv
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A black precipitate produced by a sulfate reducing bacterium Cupidesulfovibrio sp. strain HK was investigated with multidisciplinary methods. X-ray diffraction (XRD) analysis revealed that the black precipitate was mackinawite. Cyclic voltammetry analysis showed the obvious redox peaks, and the biogenic mackinawite exhibited rechargeable properties. XRD analyses showed that the form of the rechargeable biogenic mackinawite (RBM-II) was changed by discharge and recharge treatments: Field-emission transmission electron microscope analyses revealed that lepidocrocite and amorphous iron oxide were appeared from mackinawite on discharged condition, and the three kinds of minerals were intermingled via the rechargeable treatments. Physicochemical parameters were changed regularly under the treatments, suggesting that discharge would be occurred by iron oxidation and sulfur reduction, and vice versa. These results indicated that dynamics of sulfur is important key process in rechargeable mechanism, supporting that a part of mackinawite was transformed to lepidocrocite and iron oxides, and vice versa. Microbial fuel cells (MFCs) equipped with lactate, strain HK-II and anode including RBM-II consumed lactate even under opened circuit conditions, after which MFCs generated higher current density at re-closed circuit conditions. These results demonstrated that the biogenic mackinawite is one of rechargeable materials and would play important roles in geomicrobiological reactions and biotechnology.

5
A comparison study between liquid- and vapor-fed anode zero-gap bioelectrolysis cells

Rohbohm, N.; Angenent, L. T.

2024-12-22 bioengineering 10.1101/2024.12.21.629895 medRxiv
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Improving microbial electrosynthesis could be one solution for transitioning towards sustainable chemical production, offering a pathway to convert CO2 into valuable commodities from renewable energy sources. Therefore, we examined the performance differences between liquid- and vapor-fed anode zero-gap bioelectrochemical cells for electromethanogenesis, utilizing a membrane electrode assembly to enhance mass and ohmic transport. Focusing on CH4 and H2 production, we compared two ion-exchange membranes with the liquid-fed anode system and selected the best performing ion-exchange membrane for the vapor-fed anode system. Liquid-fed anode systems did not show significant differences in volumetric CH production rates compared to vapor-fed anode systems, although the latter demonstrated advantages in reducing electrocatalyst degradation and maintaining stable cell voltages. The research underscores the need for further optimization to address performance losses and suggests potential for industrial applications of microbial electrosynthesis, highlighting the importance of catalyst protection.

6
Food waste as a resource: grinding, dilution, and storage as a pretreatment strategy to produce fermentation intermediates

Daly, S.; Usack, J. G.; Harroff, L. A.; Booth, J. G.; Keleman, M. P.; Angenent, L. T.

2020-04-28 bioengineering 10.1101/2020.04.27.064808 medRxiv
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In several states of the U.S., one measure to mitigate greenhouse-gas emissions has been to ban food wastes from landfills. As a result, U.S.-based companies are now providing decentralized food-waste management systems for supermarkets and restaurants, which include storage as a slurry. It is unclear, however, which storage conditions (factors) would affect the spontaneous microbial activity, resulting in a different fermentation product spectra, and how this would affect further post-treatment. Here, we performed two experiments to mimic: 1) storage and 2) subsequent anaerobic digestion. For the food-waste storage system, we designed a mixed-level fractional factorial analysis with 12 experimental combinations, including separating food waste into: carbohydrate-rich, lipid-rich, and protein-rich food waste. We found that all factors that we tested correlated with the fermentation product spectra, but that especially the factors: i) storage temperature; ii) food-waste composition; and iii) storage time affected the fermentation outcome. We observed that relatively low pH levels of 3-4, which were achieved due to rapid lactic acid accumulation by microbial activity during storage, coincided with greater lactate production at a maximum chemical oxygen demand (COD) selectivity of 90%. This provides an opportunity to optimize lactate production, which is ideal for subsequent methane or chemical production. TOC/Abstract graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

7
Synthetic bacterial consortium for degradation of plastic pyrolysis oil waste

Jia, Y.; Dou, J.; Ballerstedt, H.; Blank, L. M.; Xing, J.

2024-04-23 bioengineering 10.1101/2024.04.21.590079 medRxiv
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The plasic crisis is ominipresent, from littering macroplastic to reports that document plastic in every niche of this planet, including the human body. In order to achieve higher recycling quotas, especially of mixed plastic waste, pyrolysis seems to be a viable option. However, depending on the process parameters, plastic pyrolysis oil waste is encountered, which is difficult to valorize, due to the enormous spread of the molecules included. To reduce the molecular heterogeneity, we here artificially compounded, monitored, and optimized the performance of a bacterial consortium, which has the ability to tolerate organic pollutants and use them as energy and carbon sources for their own metabolic activity. The primary constituents of the here used plastic pyrolysis oil waste (PPOW) were alkanes and {varepsilon}-caprolactam. The bacterial community exhibited noteworthy efficacy in eliminating alkanes of diverse chain lengths ranging from 71% to 100%. Additionally, within 7-days, the microbial community demonstrated a removal efficiency surpassing 50% for various aromatic hydrocarbons, along with complete eradication of {varepsilon}-caprolactam and naphthalene. Besides, a back-propagation (BP) neural network method is applied to evaluate O2 consumption as a measure of microbial activity. The insights gained were used to build a model, which is able to predict O2 depletion in long-time experiments and other experimental conditions. The results are discussed in the context of a developing (open) circular plastic economy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/590079v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@628f68org.highwire.dtl.DTLVardef@b5274eorg.highwire.dtl.DTLVardef@1278ceaorg.highwire.dtl.DTLVardef@194887a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LISynthetic bacterial communities are used to remove plastic hydrolysis oil waste C_LIO_LIThe optimized biphase reaction system can remove the majority of pollutants C_LIO_LIThe biodegradation process can be monitored in a real-time bioprocess software C_LIO_LINeural network techniques are used to model and predict the removal process C_LI

8
Dairy wastewater grease stabilizes in situ mesophilic biomethanation for H2-to-CH4 conversion

Ruiz-Lorenzo, M. L.; Angela, L.-Z.; Moreno, A. D.; Ferrari, F.; Diaz, I.; Contreras, J.; Iglesias, R.; Suarez, S.; Acedos, M. G.

2026-06-11 bioengineering 10.64898/2026.06.09.731101 medRxiv
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Power-to-Gas technologies are emerging as a key strategy to integrate surplus renewable electricity into energy systems, through the conversion of green hydrogen into methane. However, the practical implementation of biological in situ biomethanation is still constrained by operational and design requirements that are incompatible with most existing anaerobic digestion infrastructures. This study demonstrates a stable and efficient mesophilic (37{degrees}C) in situ biomethanation process driven by substrate-induced microbial selection rather than relying on continuous hydrogen supply. Anaerobic digesters co-digesting sewage sludge from a wastewater treatment plant with lipid-rich greases recovered from dairy wastewater developed a pre-adapted hydrogenotrophic consortium capable of effective CO2-H2 conversion under mesophilic conditions. Long-term operation confirmed the robustness and persistence of this microbial structure. Upon H2 addition, methane concentrations up to 82 % were achieved under atmospheric pressure, without biogas recirculation, with hydrogen-to-methane conversion efficiencies up to 90% and methane productivities of 1.64 NLCH4.L-1d-1. 16SrRNA-based microbial community analysis revealed that dairy grease co-digestion selectively enriched hydrogenotrophic methanogens, particularly Methanospirillum, together with syntrophic fatty-acid-degrading bacteria such as Syntrophomonas, promoting efficient interspecies hydrogen transfer. Importantly, the lipid co-substrate enabled the establishment and long-term stability of the hydrogenotrophic pathway independently of hydrogen availability, mitigating challenges associated with intermittent renewable energy supply. Overall, these findings challenge the common reliance on thermophilic conditions, continuous hydrogen input, pressurization, and gas recirculation in in situ biomethanation, demonstrating that substrate-driven microbial selection can replace conventional engineering requirements such as thermophilic operation or reactor modifications, providing a simpler and scalable strategy for mesophilic in situ biomethanation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/731101v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@c62086org.highwire.dtl.DTLVardef@1813ed6org.highwire.dtl.DTLVardef@4462bcorg.highwire.dtl.DTLVardef@1ae2cfb_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Highlights- Lipid-assisted co-digestion promotes stable biogas and biomethane production - Dairy wastewater greases enable mesophilic in situ biomethanation - An enriched hydrogenotrophic methanogenic consortium yields >82% CH4 - 70-90% H2-to-CH4 conversion efficiency under mesophilic, unpressurized conditions - Substrate-driven microbial selection enables in situ biomethanation in WWTP digesters

9
Long-term Production and Recovery of Medium-Chain Carboxylates from Source-Separated Organics

Dyussekenova, D.; Parmar, J. K.; Ezabadi, M. A.; Lindner, B. G.; Hong, Y.; Werber, J. R.; Lawson, C. E.

2026-03-27 bioengineering 10.64898/2026.03.25.714070 medRxiv
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Source-separated organics (SSO) are widely processed via anaerobic digestion to produce biogas, yet alternative conversion pathways could generate higher-value products. Here, we demonstrate long-term continuous production and recovery of medium-chain carboxylic acids (MCCAs) from SSO via microbial chain elongation using a bench-scale anaerobic bioreactor operated for 911 days. The reactor was fed with SSO samples collected from two full-scale municipal organics processing facilities in Toronto, Canada, capturing facility-specific and seasonal variability in SSO composition. MCCA production depended strongly on the availability of lactate as an electron donor, which varied with SSO preprocessing operations and outdoor collection temperatures. To mitigate product inhibition, an in-line extraction system using hollow-fiber polydimethylsiloxane (PDMS, also known as silicone) membranes was integrated with the anaerobic membrane bioreactor, providing a robust and solvent-free alternative to solvent-based extraction methods. Maximum MCCA yields reached 0.31 g MCCA/ g VSfeed, with notable octanoic acid production (up to 20% of total MCCA), and production rates up to 0.84 g L-1 d-1. Acidification of the alkaline extract produced a phase-separated MCCA-rich oil ([~]95% purity) without addition of downstream separation steps. Microbial community analysis of the reactor revealed enrichment of putative chain-elongating bacteria, including Eubacterium and Pseudoramibacter species, while shifts in SSO feedstock microbiomes influenced substrate availability and product spectra. These results demonstrate the feasibility of sustained MCCA production from municipal organic waste streams and highlight opportunities to integrate chain elongation with existing anaerobic digestion infrastructure.

10
Discovering Plastic-Binding Peptides with Favorable Affinity, Water Solubility, and Binding Specificity Through Deep Learning and Biophysical Modeling

Tan, T.; Bergman, M.; Hall, C. K.; You, F.

2026-04-01 biophysics 10.64898/2026.03.30.715295 medRxiv
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Microplastic (MP) pollution, which is present in the ecosystem in vast quantities, adversely affects human health and the environment, making it imperative to develop methods for its mitigation. The challenge of detecting or capturing MPs could potentially be addressed using plastic-binding peptides (PBPs). The ideal PBP for MP remediation would not only bind strongly to plastic, but also have other properties such as high solubility in water or great binding specificity to a certain plastic. However, the scarcity or absence of known PBPs for common plastics along with the lack of methods that can discover PBPs with all of the desired properties precludes the development of peptide-based MP remediation strategies. In this study, we discovered short linear PBPs with high predicted water solubility and binding specificity by employing an in-silico discovery pipeline that combines deep learning and biophysical modeling. First, a long short-term memory (LSTM) network was trained on biophysical modeling data to predict peptide affinity to plastic. High affinity peptides were generated by pairing the trained LSTM with a Monte Carlo tree search (MCTS) algorithm. Molecular dynamics (MD) simulations showed that the PBPs discovered for polyethylene, the most common plastic, had 15% lower binding free energy than PBPs obtained using biophysical modeling alone. PBPs with both high affinity and high predicted solubility in water were found by including the CamSol solubility score in the MCTS peptide scoring function, increasing the average solubility score from 0.2 to 0.9, while only minimally decreasing affinity for polyethylene. The framework also discovered peptides with high binding specificity between polystyrene and polyethylene, two major constituents of MP pollution, using a competitive MCTS approach that optimized the difference in affinity between the two plastics. MD simulations showed that competitive MCTS increased the binding specificity of PBPs for polystyrene and identified peptides with relatively great preference for either of the two plastics. The framework can readily be applied to design PBPs for other types of plastic. Overall, the high-affinity PBPs with desirable properties discovered by marrying artificial intelligence and biophysics can be valuable for remediating MP pollution and protecting the health of humans and the environment.

11
Design and validation of a new flat-sheet membrane bioreactor system for bioprocessing research requiring very low gas fluxes

Zhou, M.; Bello, I. O.; Magdalena, J. A.; Usack, J. G.

2025-04-15 bioengineering 10.1101/2025.04.15.649005 medRxiv
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Precise and consistent gas dosing at trace levels remains a significant challenge in bioprocessing and biotechnology research. This study introduces a novel flat-sheet membrane bioreactor for controlled gas delivery without bubble formation. The system relies on gas diffusion mediated by interchangeable membrane cassettes and incorporates mechanical stirring near the membrane surface to promote gas dispersal and mitigate biofouling spanning long operating periods. Comprehensive characterization of mass transfer properties using oxygen gas as a test case revealed that the volumetric mass transfer coefficient (KLa) remained stable under varying operational conditions, including gas partial pressure, back pressure, and total gas flow rate. The maximum oxygen flux under specific operational conditions flexibly ranged from 15.9E-03 {+/-} 6.3E-03 mol{middle dot}min-1 to 1.08 {+/-} 0.17 mol{middle dot}min-1 for various porous membranes and from 23.3E-03 {+/-} 3.5E-03 mol{middle dot}min-1 to 0.161 {+/-} 0.044 mol{middle dot}min-1 for the non-porous membranes, indicating the bioreactor can serve as an experimental platform for a variety of applications. A biological validation study using starch-containing wastewater demonstrated the feasibility of continuous microaerobic oxygen dosing, achieving reproducible performance and maintaining stable operation over 320 days. These findings highlight the potential of the developed system as a reliable experimental platform for investigating bioprocesses dependent on trace gas supply. Future improvements should focus on scaling up the system, addressing porous membrane wetting, and expanding its applicability to other gases and bioprocessing applications.

12
Equipment-Free Personal Protective Equipment (PPE) Fabrication from Bacterial Cellulose-Derived Biomaterials via Waste-to-Wealth Conversion

Veerubhotla, R.; Bandopadhyay, A.; Chakraborty, S.

2022-11-03 bioengineering 10.1101/2022.11.02.514716 medRxiv
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The recent COVID-19 crisis necessitated the universal use of Personal Protection Equipment (PPE) kits, generating tons of plastic wastes that inevitably lead to environmental damage. Circumventing the challenges stemming from such undesirable non-degradability on disposal, here we present an eco-friendly, robust, yet inexpensive and equipment-free method of growing biodegradable PPE fabrics by the fermentation of locally-sourced organic feed stocks in a rural livelihood. Using a pre-acclimatized symbiotic culture, we report the production of a high yield (up to 3.2 g fabric/g substrate) of bacterial cellulose, a biopolymer matrix, obtained by bacterial weaving. This membrane has an intricate, self-assembled, nano-porous 3D architecture formed by randomly oriented cellulose fibres. Scanning electron microscopy reveals that the pore size of the membrane turns out to be in the tune of 140 nanometers on the average, indicating that it can filter out viruses effectively. In-vitro results demonstrate assured breathability through the membrane for a filter thickness of approximately 5 microns. When subjected to soil degradation, the fabrics are seen to disintegrate rapidly and fully decompose within 15 days. With a favourable cost proposition of less than 1 US$ per meter square of the developed fabric unit, our approach stands out in providing a unique sustainable, and production-ready alternative to synthetic PPE fabrics, solving community healthcare and environmental crisis, and opening up new avenues sustainable under-served livelihood at the same time. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/514716v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@bfa2forg.highwire.dtl.DTLVardef@5649a3org.highwire.dtl.DTLVardef@fc99a4org.highwire.dtl.DTLVardef@1cae297_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Enhanced Hydrogen Production Through Two-Stage Fermentation Coupling Clostridium pasteurianum and Rhodobacter sphaeroides

Tan, G.-Y.; zhang, x.; Wang, w. h.; Cheng, f. Y.; Zhang, X.; fan, h. J.; Zhang, L.; Ye, l. X.

2025-12-16 bioengineering 10.64898/2025.12.14.694164 medRxiv
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Biological H2 production via dark fermentation is constrained by low yields and inhibitory metabolite accumulation. Coupling dark and photo fermentation effectively overcomes these issues by enhancing substrate utilization and reducing wastewater pollution, yet scalable systems for industrial application remain rare. This study presents a 10-L two-stage fermentation system (5L dark/5L photo bioreactors) using Clostridium pasteurianum DSM 525 and Rhodobacter sphaeroides ZX-5. Dark fermentation generated 3372 mL H2 from glucose, yielding effluent with 1.29 g/L acetic and 3.11 g/L butyric acids. After centrifugation, pH adjustment, and clinoptilolite deamination ([&ge;]60% efficiency), ammonium was reduced to <100 mg/L. The pretreated effluent, supplemented with concentrated RCVBN medium, served as photo-fermentation substrate. A butyric acid feeding strategy extended the process by 120 h, boosting H2 yield by 16.4%. The coupled system produced 6480 mL H2 (80% increase), degrading 50% acetic acid and 42% butyric acid. This work demonstrates a scalable bioreactor configuration integrating efficient biohydrogen production with value-added wastewater treatment for industrial bioenergy applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/694164v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1f324a4org.highwire.dtl.DTLVardef@1eab711org.highwire.dtl.DTLVardef@98e50dorg.highwire.dtl.DTLVardef@1e5f02e_HPS_FORMAT_FIGEXP M_FIG Graphic abstract C_FIG

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High-throughput screening and selection of PCB-bioelectrocholeaching, electrogenic microbial communities using single chamber microbial fuel cells based on 96-well plate array.

SZYDLOWSKI, L.; Ehlich, J.; Shibata, N.; Goryanin, I.

2021-06-10 bioengineering 10.1101/2021.06.09.447729 medRxiv
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We demonstrate a single chamber, 96-well plate based Microbial Fuel Cell (MFC). This invention is aimed at robust selection of electrogenic microbial community under specific conditions, (pH, external resistance, inoculum) that can be altered within the 96 well plate array. Using this device, we selected and multiplicated electrogenic microbial communities fed with acetate and lactate that can operate under different pH and produce current densities up to 19.4 A/m3 (0.6 A/m2) within 5 days past inoculation. Moreover, studies shown that Cu mobilization through PCB bioleaching occurred, thus each community was able to withstand presence of Cu2+ ions up to 600 mg/L. Metagenome analysis reveals high abundance of Dietzia spp., previously characterized in MFCs, but not reported to grow at pH 4, as well as novel species, closely related to Actinotalea ferrariae, not yet associated with electrogenicity. Microscopic observations (combined SEM and EDS) reveal that some of the species present in the anodic biofilm were adsorbing copper on their surface, probably due to the presence of metalloprotein complexes on their outer membranes. Taxonomy analysis indicated that similar consortia populate anodes, cathodes and OCP controls, although total abundances of aforementioned species are different among those groups. Annotated metagenomes showed high presence of multicopper oxidases and Cu-resistance genes, as well as genes encoding aliphatic and aromatic hydrocarbon-degrading enzymes. Comparison between annotated and binned metagenomes from pH 4 and 7 anodes, as well as their OCP controls revealed unique genes present in all of them, with majority of unique genes present in pH 7 anode, where novel Actinotalea spp. was present.

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Steering the chain-elongating microbiome to specific medium-chain carboxylates with ethanol and lactate as co-electron donors: maximizing C8 or C6

Wang, H.; Jeon, B. S.; Ortiz-Ardila, A.; Angenent, L. T.

2025-02-08 bioengineering 10.1101/2025.02.07.637006 medRxiv
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Microbial chain elongation is a sustainable process to convert organic residues into valuable biochemicals via anaerobic fermentation. The operating conditions for the bioreactor and the ecological interactions among functional populations are crucial in controlling this process, but they have not been completely ascertained. Here, we unraveled two operating conditions (i.e., environmental factors): (1) the substrate ratio of ethanol and lactate as co-electron donors, and (2) the temperature, which affected both the product specificity (i.e., function) and microbial dynamics of chain-elongating microbiomes in a continuously fed bioreactor with product extraction. Specifically, we found that the increase in the substrate ratio of ethanol to lactate shifted the microbiomes toward n-caprylate (C8) production, while the slightly higher operating temperatures of 37{degrees}C or 42{degrees}C were advantageous to n-caproate (C6) production. We detected a core microbiome that was similar for all environmental conditions and the two bioreactors, consisting of populations from Sphaerochaeta spp., Caproiciproducens spp., and Oscillospiraceae. Besides the core microbiome, we observed positive correlations between Erysipelaclostridiaceae UCG-004, Bacteroides spp., Oscillospiraceae NK4A214, Rikenellaceae RC9, and Pseudoclavibacter spp. with n-caprylate production. Similar populations compared to the core microbiome were positively correlated with n-caproate production. We showed that we can steer microbiomes toward a high specificity of certain medium-chain carboxylates. Abstract Graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/637006v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@70557eorg.highwire.dtl.DTLVardef@fcee81org.highwire.dtl.DTLVardef@18e64feorg.highwire.dtl.DTLVardef@1888a8d_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISGenerating medium-chain carboxylates is a promising open-culture biotechnology production platform for converting organic waste streams into biofuels and chemicals.

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Dried-bakery waste as a substrate for n-caproate and n-caprylate production via chain elongation: bakeroate

Ntihuga, J. N.; Usack, J.; Mayer, R.; Kinbokun, A. A.; Yesil, H.; Zhou, M.; Angenent, L. T.

2025-12-31 bioengineering 10.64898/2025.12.20.695658 medRxiv
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Bakery waste is a promising feedstock for the circular economy; however, its use for producing medium-chain carboxylates (MCCs) via microbial chain elongation remains unexplored. This study investigated pretreatment, pertraction, and chain elongation strategies to convert bakery waste into n-caproate and n-caprylate. Bakery waste was mechanically and enzymatically processed, and different inocula were tested to optimize the conversion of the resulting glucose-rich solution into lactate and ethanol (intermediates). These intermediates were fed into continuous chain elongation systems, which operated for over 386 days at 37{degrees}C and pH 5.5. Results showed that 30-35% of bakery waste carbon was converted into n-caproate and 10-15% into n-caprylate. Enzymatic starch hydrolysis proved essential, and lactate was a superior intermediate for chain elongation compared to ethanol. A maximum volumetric MCC production rate of 131 mM C L-1 d-1 (0.1 g L-1 h-1) was achieved. This integrated approach, named "bakeraote," demonstrates an efficient pathway for valorizing bakery waste.

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Over four months of ethylene production: Unlocking the potential of solid-state photosynthetic cell factories

Kosourov, S.; Siitonen, V.; Toth, G.; Leva, T.; Tammelin, T.; Kallio, P.; Allahverdiyeva, Y.

2025-09-17 bioengineering 10.1101/2025.09.12.675104 medRxiv
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This study demonstrates the feasibility of employing solid-state photosynthetic cell factories (solid-state PCFs) as a proof-of-concept platform for long-term ethylene production using sodium bicarbonate as the carbon source. Solid-state PCFs were constructed by entrapping Synechocystis sp. PCC 6803 (efe mutant, strain S5), specifically engineered for ethylene biosynthesis, within TEMPO-oxidized cellulose nanofiber (TCNF) matrices. Two distinct formulations were tested: (i) Ca2+-PVA-TCNF, in which TCNF was crosslinked with Ca2+ and polyvinyl alcohol to produce hydrogel films approximately 200 m thick; and (ii) an all-polysaccharide-based Ca2+-MLG-TCNF formulation, in which TCNF was crosslinked with Ca2+ and mixed-linkage glucan. The latter films were fabricated using an osmotic dehydration approach, yielding mechanically robust, fully biodegradable structures with a thickness of approximately 2 mm. The integration of engineered cells with TCNF matrices created a biocatalytic system that improved the distribution of light, nutrients, and substrates to the cells, while facilitating ethylene separation, thereby supporting the fitness of immobilized cells and enhancing their metabolic performance. Using a custom-designed photobiofilm reactor optimized for semi-wet cultivation, the solid-state PCFs sustained ethylene production for over four months, representing the longest reported continuous ethylene production by cyanobacteria to date. Notably, the solid-state PCFs achieved up to a twofold increase in ethylene yield compared to the continuous-flow suspension culture. Importantly, the suspension-based system also represented the first demonstration of four-month ethylene production under continuous-flow operation. In addition, biodegradability assessments confirmed the environmental compatibility of the TCNF-based matrices, with the all-polysaccharide formulation being particularly advantageous due to its exclusively nature-based composition. Together, these results demonstrate the potential of solid-state PCFs as a scalable and sustainable platform for photosynthetic ethylene production.

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Establishment Strategy and Temporal Dynamics of Tetrasphaera-Enriched Microbiome for Enhanced Biological Phosphorus Removal and Recovery

Wang, H.; Wang, Y.; Zhang, G.; Zhao, Z.; Ju, F.

2022-08-23 bioengineering 10.1101/2022.08.23.504879 medRxiv
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Tetrasphaera were recently identified based on the 16S rRNA gene as among the most abundant polyphosphate-accumulating organisms (PAOs) in global full-scale wastewater treatment plants (WWTPs) with enhanced biological phosphorus removal (EBPR). However, it is unclear how Tetrasphaera PAOs are selectively enriched in the context of the EBPR microbiome. In this study, an EBPR microbiome enriched with Tetrasphaera (accounting for 40% of 16S sequences on day 113) was built using a top-down design approach featuring multicarbon sources and a low dosage of allylthiourea. The microbiome showed enhanced nutrient removal (P removal ~85% and N removal ~80%) and increased P recovery (up to 23.2 times) compared with the seeding activated sludge from a local full-scale WWTP. The supply of 1 mg/L allylthiourea promoted the coselection of Tetrasphaera PAOs and Microlunatus PAOs and sharply reduced the relative abundance of both ammonia oxidizer Nitrosomonas and putative competitors Brevundimonas and Paracoccus, facilitating the establishment of the EBPR microbiome. Based on 16S rRNA gene analysis, a putative novel PAO species, EBPR-ASV0001, was identified with Tetrasphaera japonica as its closest relative. This study provides new knowledge on the establishment of a Tetrasphaera-enriched microbiome facilitated by allylthiourea, which can be further exploited to guide future process upgrading and optimization to achieve and/or enhance simultaneous biological phosphorus and nitrogen removal from high-concentration wastewater.

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A decision-making tool to navigate through Extracellular Vesicle research and product development

Loria, F.; Picciotto, S.; Adamo, G.; Zendrini, A.; Raccosta, S.; Manno, M.; Bergese, P.; Liguori, G. L.; Bongiovanni, A.; Zarovni, N.

2023-11-17 cell biology 10.1101/2023.11.16.567368 medRxiv
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Due to their intercellular communication properties and their involvement in a wide range of biological processes, extracellular vesicles (EVs) are increasingly being studied and exploited for different applications. Nevertheless, their complex nature and heterogeneity, as well as the challenges related to their isolation, purification and characterization procedures, require cautious assessment of the quality and quantity parameters to monitor. This translates into a multitude of choices and putative solutions that lie in front of any EV researcher, in both research and translational environments, resembling a labyrinth with multiple paths to cross and, possibly, more than one exit. In this respect, decision-making tools might represent our modern Ariadnes string to follow not to get lost or distracted along the journey, to choose the shorter and best-fit-to-source EV application(s) and vice versa. Here, we present the implementation of a multi-criteria EV decision-making grid (EV-DMG) as a novel, customizable, efficient and easy-to-use tool to support responsible EV research and innovation. By identifying and weighting key assessment criteria for comparing distinct EV-based preparations and/or processes, our EV-DMG may assist any EV community member in making informed, transparent and reproducible decisions regarding the EV sources and/or samples to be managed, as well as the most suitable production and/or analytical pipelines to be adopted for targeting a defined aim or application.

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Oxic microbial electrosynthesis can be more energy efficient for biomass production than knallgas or photosynthesis based processes

Rominger, L.; Hackbarth, M.; Jung, T.; Scherzinger, M.; Horn, H.; Kaltschmitt, M.; Gescher, J.

2023-05-24 bioengineering 10.1101/2023.05.24.542149 medRxiv
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Data on the efficiency and development of continuous processes are scarce in the emerging field of oxic microbial electrosynthesis (OMES). Therefore, the recently isolated knallgas bacterium Kyrpidia spormannii was observed in a bioelectrochemical flow cell setup to study biomass formation and energy efficiency of cathode dependent growth. The study revealed that a potential of -500 mV vs. the standard hydrogen electrode (SHE) caused differences in the structure of the biofilm developing on the cathode, but had almost no impact on biomass growth behavior compared to -375 mV vs. SHE. No growth was observed at 0 mV vs SHE. Coulombic efficiency (CE) was calculated for the cultivation at -500 mV vs. SHE. The process can be conducted with the same electron efficiency as traditional gas fermentation. The solar energy demand with 67.89 kWh kg-1 dry biomass is highly competitive to alternative and already established processes for converting (solar) energy to biomass. Additionally, with suggestions for a biomass harvesting method and subsequent recultivation, proof of principle for a continuously operable process was provided. The results pave the way for a new concept in carbon dioxide-based biotechnology. Significance statementTo mitigate global climate change, it is imperative to transition the human economy to a different resource foundation, moving away from fossil fuels and reducing atmospheric carbon dioxide levels. Biotechnological production based on CO2 necessitates a supply of energy and electrons. This study reveals that an oxic process, wherein bacteria are directly cultivated as a biofilm on the cathode surface of a bioelectrochemical system, can exhibit higher energy efficiency than plant-based systems or systems reliant on hydrogen generated through water electrolysis. This technology could be instrumental in establishing carbon dioxide and renewable energy as the foundation for feed, food, and platform chemical production.