Medium Chain Carboxylic Acids from Complex Organic Feedstocks by Mixed Culture Fermentation

Comprehensive review of microbial production of medium-chain fatty acids from waste activated sludge and enhancement strategy

Microbial production of versatile applicability medium-chain fatty acids (MCFAs) (C6-C10) from waste activated sludge (WAS) provides a pioneering approach for wastewater treatment plants (WWTPs) to achieve carbon recovery. Mounting studies emerged endeavored to promote the MCFAs production from WAS while struggling with limited MCFAs production and selectivity. Herein, this review covers comprehensive introduction of the transformation process from WAS to MCFAs and elaborates the mechanisms for unsatisfactory MCFAs production. The enhancement strategies for biotransformation of WAS to MCFAs was presented. Especially, the robust performance of iron-based materials is highlighted. Furthermore, knowledge gaps are identified to outline future research directions. Recycling MCFAs from WAS presents a promising option for future WAS treatment, with iron-based materials emerging as a key regulatory strategy in advancing the application of WAS-to-MCFAs biotechnology. This review will advance the understanding of MCFAs recovery from WAS and promote sustainable resource management in WWTPs.

Recent progress and prospects for chain elongation of transforming biomass waste into medium-chain fatty acids

Chain elongation technology utilises microorganisms in anaerobic digestion to transform waste biomass into medium-chain fatty acids that have greater economic value. This innovative technology expands upon traditional anaerobic digestion methods, requiring abundant substrates that serve as electron donors and acceptors, and inoculating microorganisms with chain elongation functions. While this process may result in the production of by-products and elicit competitive responses, toxicity suppression of microorganisms by substrates and products remains a significant obstacle to the industrialisation of chain elongation technology. This study provides a comprehensive overview of existing research on widely employed electron donors and their synthetic reactions, competitive reactions, inoculum selection, toxicity inhibition of substrates and products, and increased chain elongation approaches. Additionally, it presents actionable recommendations for future research and development endeavours in this domain, intending to inspire and guide researchers in advancing the frontiers of chain elongation technology.

Efficient caproic acid production from lignocellulosic biomass by bio-augmented mixed microorganisms

Producing caproic acid via carboxylate platform is an environmentally-friendly approach for treating lignocellulosic agricultural waste. However, its implementation is still challenged by low product yields and selectivity. A microbiome named cellulolytic acid-producing microbiome (DCB), proficient in producing cellulolytic acid, was successfully acquired and shows promise for producing high-level caproic acid. In this study, a bioaugmentation method utilizing Clostridium kluyveri is proposed to enhance caproic acid yield of DCB using rice straw. With exogenous ethanol, bioaugmentation with Clostridium kluyveri significantly improved the caproic acid concentration and selectivity by 7 times and 4.5 times, achieving 12.9 g/L and 55.1 %, respectively. The addition of Clostridium kluyveri introduced reverse β-oxidation pathway, a more efficient caproic acid production pathway. Meanwhile, bioaugmentation enriched the bacteria proficient in degrading straw and producing short-chain fatty acids, providing more substrates for caproic acid production. This study provides potential bioaugmentation strategies for optimizing caproic acid yield from lignocellulosic biomass.

Influence of pH and temperature on the performance and microbial community during the production of medium-chain carboxylic acids using winery effluents as substrate

Winery effluents containing high ethanol concentrations and diverse organic matter are ideal substrates for producing medium-chain carboxylic acids via fermentation and chain elongation. However, the process needs to be better understood. This study presents novel insights into the bioconversion mechanisms of medium-chain carboxylic acids by correlating fermentation and chain elongation kinetic profiles with the study of microbial communities at different pH (5 to 7) conditions and temperatures (30 to 40 °C). It was found that high productivities of MCCA were obtained using a native culture and winery effluents as a natural substrate. Minor pH variations significantly affected the metabolic pathway of the microorganisms for MCCA production. The maximal productivities of hexanoic (715 mg/L/d) and octanoic (350 mg/L/d) acids were found at pH 6 and 35 °C. Results evidence that the presence of Clostridium, Bacteroides, and Negativicutes promotes the high productions of MCCA. The formation of heptanoic acid was favor when Mogibacterium and Burkholderia were present.

CO2 uptake in ethanol-driven chain elongation system: Microbial metabolic mechanisms

CO2 as a byproduct of organic waste/wastewater fermentation has an important impact on the carboxylate chain elongation. In this study, a semi-continuous flow reactor was used to investigate the effects of CO2 loading rates (Low = 0.5 LCO2·L-1·d-1, Medium = 1.0 LCO2·L-1·d-1, High = 2.0 LCO2·L-1·d-1) on chain elongation system Ethanol and acetate were utilized as the electron donor and electron acceptor, respectively. The results demonstrate that low loading rate of CO2 has a positive effect on chain elongation. The maximum production of caproate and CH4 were observed at a low CO2 loading rate. Caproate production reached 1.88 g COD·L-1·d-1 with a selectivity of 62.55 %, while CH4 production reached 129.7 ml/d, representing 47.4 % of the total. Metagenomic analysis showed that low loading rate of CO2 favored the enrichment of Clostridium kluyveri, with its abundance being 3.8 times higher than at of high CO2 loading rate. Metatranscriptomic analysis revealed that high CO2 loading rate induced oxidative stress in microorganisms, as evidenced by increased expression of heat shock proteins and superoxide dismutase genes. Further investigation suggested that genes associated with the reverse β-oxidation pathway, CO2 uptake pathway and hydrogenotrophic methanogenesis pathway were reduced at high CO2 loading rate. These findings provide insight into the underlying mechanisms of how CO2 affects chain elongation, and it could be a crucial reason for the poor performance of chain elongation systems with high endogenous CO2 production.

Advances in understanding entire process of medium chain carboxylic acid production from organic wastes via chain elongation

Chain elongation is an environmentally friendly biological technology capable of converting organic wastes into medium chain carboxylic acids (MCCAs). This review aims to offer a comprehensive analysis of MCCA production from organic wastes via chain elongation. Seven kinds of organic wastes are introduced and classified as easily degradable and hardly degradable. Among them, food waste, fruit and vegetable waste are the most potential organic wastes for MCCA production. Combined pretreatment technologies should be encouraged for the pretreatment of hardly degradable organic wastes. Furthermore, the mechanisms during MCCA production are analyzed, and the key influencing factors are evaluated, which affect the MCCA production and chain elongation efficiency indirectly. Extracting MCCA simultaneously is the most important way to improve MCCA production efficiency, and technologies for sequentially extracting different kinds of MCCAs are recommended. Finally, some perspectives for future chain elongation researches are proposed to promote the large-scale application of chain elongation.

Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting

As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R² > 0.87) and intermediate accuracy in the near future (R² > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.

Co-fermenting lactic acid and glucose towards caproic acid production

The functional role of lactate (H_Lac), as a co-substrate along with glucose (Glu) as well as an electron donor for the synthesis of caproic acid (H_Ca), a medium chain fatty acid (MCFAs) was studied. A varied H_Lac and Glu ratios were thus investigated in fed-batch anaerobic reactors (R1-R5) operated at pH 6 with a heat-treated anaerobic consortium. R1 and R5 were noted as controls and operated with sole Glu and H_Lac, respectively. Strategically, ethanol (H_Eth) was additionally supplemented as co-electron donor after the production of short chain carboxylic acids (SCCAs) for chain elongation in all the reactors. The reactor operated with H_Lac and Glu in a ratio of 0.25:0.75 (1.25 g/L (H_Lac) and 3.75 g/L (Glu)) showed the highest H_Ca production of 1.86 g/L. R5 operated with solely H_Lac yielded propionic acid (H_Pr) as the major product which further led to the higher valeric acid (H_Va) production of 1.1 g/L within the reactor. Butyric acid (H_Bu) was observed in R1, which used Glu as carbon source alone indicating the importance of H_Lac as electron co-donor. Clostridium observed as the most dominant genera in shotgun metagenome sequencing in R2 and R3, the reactors that produced the highest H_Ca in comparison to other studied reactors. The study thus provided insight into the importance of substrate and electron donor and their supplementation strategies during the production of MCFAs.

A specific H2/CO2 consumption molar ratio of 3 as a signature for the chain elongation of carboxylates from brewer's spent grain acidogenesis

Brewer's spent grain (BSG) is an undervalorized organic feedstock residue composed of fermentable macromolecules, such as proteins, starch, and residual soluble carbohydrates. It also contains at least 50% (as dry weight) of lignocellulose. Methane-arrested anaerobic digestion is one of the promising microbial technologies to valorize such complex organic feedstock into value-added metabolic intermediates, such as ethanol, H₂, and short-chain carboxylates (SCC). Under specific fermentation conditions, these intermediates can be microbially transformed into medium-chain carboxylates through a chain elongation pathway. Medium-chain carboxylates are of great interest as they can be used as bio-based pesticides, food additives, or components of drug formulations. They can also be easily upgraded by classical organic chemistry into bio-based fuels and chemicals. This study investigates the production potential of medium-chain carboxylates driven by a mixed microbial culture in the presence of BSG as an organic substrate. Because the conversion of complex organic feedstock to medium-chain carboxylates is limited by the electron donor content, we assessed the supplementation of H₂ in the headspace to improve the chain elongation yield and increase the production of medium-chain carboxylates. The supply of CO₂ as a carbon source was tested as well. The additions of H₂ alone, CO₂ alone, and both H₂ and CO₂ were compared. The exogenous supply of H₂ alone allowed CO₂ produced during acidogenesis to be consumed and nearly doubled the medium-chain carboxylate production yield. The exogenous supply of CO₂ alone inhibited the whole fermentation. The supplementation of both H₂ and CO₂ allowed a second elongation phase when the organic feedstock was exhausted, which increased the medium-chain carboxylate production by 285% compared to the N₂ reference condition. Carbon- and electron-equivalent balances, and the stoichiometric ratio of 3 observed for the consumed H₂/CO₂, suggest an H₂- and CO₂-driven second elongation phase, converting SCC to medium-chain carboxylates without an organic electron donor. The thermodynamic assessment confirmed the feasibility of such elongation.

Butanol as a major product during ethanol and acetate chain elongation

Chain elongation is a relevant bioprocess in support of a circular economy as it can use a variety of organic feedstocks for production of valuable short and medium chain carboxylates, such as butyrate (C4), caproate (C6), and caprylate (C8). Alcohols, including the biofuel, butanol (C4), can also be generated in chain elongation but the bioreactor conditions that favor butanol production are mainly unknown. In this study we investigated production of butanol (and its precursor butyrate) during ethanol and acetate chain elongation. We used semi-batch bioreactors (0.16 L serum bottles) fed with a range of ethanol concentrations (100-800 mM C), a constant concentration of acetate (50 mM C), and an initial total gas pressure of ∼112 kPa. We showed that the butanol concentration was positively correlated with the ethanol concentration provided (up to 400 mM C ethanol) and to chain elongation activity, which produced H₂ and further increased the total gas pressure. In bioreactors fed with 400 mM C ethanol and 50 mM C acetate, a concentration of 114.96 ± 9.26 mM C butanol (∼2.13 g L^-1) was achieved after five semi-batch cycles at a total pressure of ∼170 kPa and H₂ partial pressure of ∼67 kPa. Bioreactors with 400 mM C ethanol and 50 mM C acetate also yielded a butanol to butyrate molar ratio of 1:1. At the beginning of cycle 8, the total gas pressure was intentionally decreased to ∼112 kPa to test the dependency of butanol production on total pressure and H₂ partial pressure. The reduction in total pressure decreased the molar ratio of butanol to butyrate to 1:2 and jolted H₂ production out of an apparent stall. Clostridium kluyveri (previously shown to produce butyrate and butanol) and Alistipes (previously linked with butyrate production) were abundant amplicon sequence variants in the bioreactors during the experimental phases, suggesting the microbiome was resilient against changes in bioreactor conditions. The results from this study clearly demonstrate the potential of ethanol and acetate-based chain elongation to yield butanol as a major product. This study also supports the dependency of butanol production on limiting acetate and on high total gas and H₂ partial pressures.

Thermocaproicibacter melissae gen. nov., sp. nov., a thermophilic chain-elongating bacterium, producing n-caproate from polymeric carbohydrates

Strain MDTJ8^T is a chain-elongating thermophilic bacterium isolated from a thermophilic acidogenic anaerobic digestor treating human waste while producing the high commodity chemical n-caproate. The strain grows and produces formate, acetate, n-butyrate, n-caproate and lactate from mono-, di- and polymeric saccharides at 37-60 °C (optimum, 50-55 °C) and at pH 5.0-7.0 (optimum, pH 6.5). The organism is an obligate anaerobe, is motile and its cells form rods (0.3-0.5×1.0-3.0 µm) that stain Gram-positive and occur primarily as chains. Phylogenetic analysis of both the 16S rRNA gene and full genome sequence shows that strain MDTJ8^T belongs to a group that consists of mesophylic chain-elongating bacteria within the family Oscillospiraceae, being nearest to Caproicibacter fermentans EA1^T (94.8 %) and Caproiciproducens galactitolivorans BS-1^T (93.7 %). Its genome (1.96 Mbp) with a G+C content of 49.6 mol% is remarkably smaller than those of other chain-elongating bacteria of the family Oscillospiraceae. Pairwise average nucleotide identity and DNA-DNA hybridization values between strain MDJT8^T and its mesophilic family members are less than 70 and 35 %, respectively, while pairwise average amino acid identity values are less than 68 %. In addition, strain MDJT8^T uses far less carbohydrate and non-carbohydrate substrates compared to its nearest family members. The predominant cellular fatty acids of strain MDTJ8^T are C_14 : 0, C_14 : 0 DMA (dimethyl acetal) and C_16 : 0, while its polar lipid profile shows three unidentified glycophospholipids, 11 glycolipids, 13 phospholipids and six unidentified lipids. No respiratory quinones and polyamines are detected. Based on its phylogenetic, genotypic, morphological, physiological, biochemical and chemotaxonomic characteristics, strain MDTJ8^T represents a novel species and novel genus of the family Oscillospiraceae and Thermocaproicibacter melissae gen. nov., sp. nov. is proposed as its name. The type strain is MDTJ8^T (=DSM 114174^T=LMG 32615^T=NCCB 100883^T).

Performance and mechanisms of medium-chain fatty acid production by anaerobic fermentation of food waste without external electron donors

This study performed a long-term operation to achieve efficient medium-chain fatty acids (MCFAs) production by anaerobic fermentation of food waste without external electron donors. The results show that total MCFAs reached the highest concentration of 29,886.10 mg COD/L, and n-caproate was the primary product, reaching the current maximum concentration of 28,191.66 mg COD/L. Microbial composition analysis demonstrated Lactobacillus, Bifidobacterium, Sporanaerobacter, and Caproiciproducens constituted the core community throughout the process. Metagenomic analysis suggested that two pathways, reverse β-oxidization (RBO) and fatty acid biosynthesis (FAB), were observed, and the FAB pathway was the main CE pathway. Unclassified_f_Ruminococcaceae and Limosilactobacillus were the main participants in the FAB pathway. This study is expected to provide new insights into MCFAs production from organic waste.

Thermophilic caproic acid production from grass juice by sugar-based chain elongation

Medium chain carboxylic acids (MCCA) such as caproic acid have a plethora of applications, ranging from food additives to bioplastics. MCCA can be produced via microbial chain elongation using waste and side-streams as substrates, a process that can be more sustainable than conventional production routes. Most chain elongation studies have focused on mesophilic conditions, with only two recent studies hinting at the possibility of thermophilic chain elongation, but a systematic study of its mechanisms is lacking. Here, we investigated thermophilic chain elongation from grass juice, to understand the effect of key operational parameters (pH, temperature, substrate) on the process performance and to establish the key microbial genera and their role in the system. The genus Caproiciproducens was identified as responsible for thermophilic chain elongation, and caproic acid production was most favorable at pH 6.0 and 50 °C among the conditions tested, reaching an average concentration of 3.4 g/L. Batch experiments showed that the substrate for caproic acid production were glucose and xylose, while lactic acid led to the production of only butyric acid. Fed-batch experiments showed that substrate availability and the presence of caproic acid in the system play a major role in shaping the profile of thermophilic chain elongation. The increase of the total sugar concentration by glucose addition (without changing the organic load) during continuous operation led to a microbial community dominated (75 %) by Caproiciproducens and increased by 76 % the final average caproic acid concentration to 6.0 g/L (13 g_COD/L) which represented 32 % (g/g) of the total carboxylic acids. The highest concentration achieved was 7.2 g/L (day 197) which is the highest concentration reported under thermophilic conditions thus far. The results of this work pave the way to the potential development of thermophilic systems for upgrading various underexplored abundant and cheap sugar-rich side-streams to caproic acid.

Prediction and optimization of medium-chain carboxylic acids production from food waste using machine learning models

Machine learning models were developed in this study to predict and optimize the medium-chain carbolic acids (MCCAs) production from food waste. All three selected prediction algorithms achieved decent performance (accuracy > 0.85, R² > 0.707). Three optimization algorithms were applied for MCCA production optimization based on the prediction algorithms. The maximum MCCA production rate (0.68 g chemical oxygen demand per liter per day) was achieved by simulated annealing coupled with random forest under the optimal conditions of pH 8.3, temperature 50 °C, retention time 4 days, loading rate 15.8 g volatile solid per liter per day, and inoculum to food waste ratio 70:30 with semi-continuous mode. Further experiments validated (18 % error) that the MCCA production rate was 113 % higher than the highest production rate of current lab experiments and 60 % higher than the statistical optimization using response surface methodology. This study demonstrates the potential of using machine learning for MCCA production prediction and optimization.

Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community

The production of volatile fatty acids (VFA) is gaining momentum due to their central role in the emerging carboxylate platform. Particularly, the production of the longest VFA (from butyrate to caproate) is desired due to their increased economic value and easier downstream processing. While the use of undefined microbial cultures is usually preferred with organic waste streams, the use of defined microbial co-culture processes could tackle some of their drawbacks such as poor control over the process outcome, which often leads to low selectivity for the desired products. However, the extensive experimentation needed to design a co-culture system hinders the use of this technology. In this work, a workflow based on the combined use of mathematical models and wet experimentation is proposed to accelerate the design of novel bioprocesses. In particular, a co-culture consisting of Pediococcus pentosaceus and Megaphaera cerevisiae is used to target the production of high-value odd- and even‑carbon VFA. An unstructured kinetic model was developed, calibrated and used to design experiments with the goal of increasing the selectivity for the desired VFA, which were experimentally validated. In the case of even‑carbon VFA, the experimental validation showed an increase of 38 % in caproate yield and, in the case of enhanced odd‑carbon VFA experiments, the yield of butyrate and caproate diminished by 62 % and 94 %, respectively, while propionate became one of the main end products and valerate yield value increased from 0.007 to 0.085 g_valearte per g_{consumed sugar.} The workflow followed in this work proved to be a sound tool for bioprocess design due to its capacity to explore and design new experiments in silico in a fast way and ability to quickly adapt to new scenarios.

Influence of lactate to acetate ratio on biological production of medium chain carboxylates via open culture fermentation

Waste valorisation via biological production of widely used in the industry medium chain carboxylates (MCCs) via open culture fermentation (OCF) could be a promising alternative to the commonly used anaerobic digestion. Lactate-rich waste streams are considered as valuable substrates for carboxylate chain elongation (CE), however, there are certain limitations related to the production efficiency. Acetate produced and accumulated in the acetogenesis plays an important role in CE, i.e. acetate is elongated to butyrate and then to caproate which is most popular MCC. Henceforth, it was investigated whether the ratio of lactate to acetate (L:A) affected carboxylates yields and product distribution in the lactate-based CE in OCF. The tested L:A ratios influenced carboxylates selectivity in batch trials. In the ones with lactate as the sole carbon source, propionate production was predominant but when a higher relative acetate concentration was used, the production of butyrate and CE to caproate was favored. The co-utilization of lactate and acetate in a continuous process increased the production of butyrate and caproate compared to the phase with lactate as the sole carbon source, however, controlling the relative concentration of lactate and acetate during co-utilization was not an effective strategy for increasing caproate production. 16S rRNA gene amplicon reads mapping to Caproiciproducens were the most abundant in samples collected throughout the continuous processes regardless of the L:A ratios.

Unveiling the bioelectrocatalyzing behaviors and microbial ecological mechanisms behind caproate production without exogenous electron donor

Bioelectrochemical systems were proposed as a promising approach for the efficient valorization of biomass into 6-8 carbon atom medium-chain fatty acids (MCFAs), the precursors for high value-added chemicals or renewable energy, via acetyl-CoA-mediated chain elongation (CE). To achieve CE processes, exogenous electron donors (EDs), e.g., ethanol or lactic acid, were normally prerequisites. This research built a microbial electrolysis cell (MEC) for MCFAs biosynthesis from acetate without exogenous EDs addition. A wide range of applied voltages (0.6-1.2 V) was first employed to investigate the bioelectrocatalyzing response. The results show that caproate and butyrate were the main products formed from acetate under different applied voltages. Maximum caproate concentration (501 ± 12 mg COD/L) was reached at 0.8 V on day 3. Under this applied voltage, hydrogen partial pressure stabilized at about 0.1 bar, beneficial for MCFA production. Electron and carbon balances revealed that the electron-accepting capacity achieved 32% at 0.8 V, showing the highest interspecies electron transfer efficiency. Most of the carbon was recovered in the form of caproate (carbon loss was 9%). MiSeq sequencing revealed Rhodobacter and Clostridium_sensu_stricto playing the crucial role in the biosynthesis of caproate, while Acetobacterium, Acetoanaerobium, and Acetobacter represented the main ED contributors. Four available flora, i.e., homo-acetogen, anaerobic fermentation bacteria, electrode active bacteria, and nitrate-reducing bacteria, interacted and promoted caproate synthesis by molecular ecological network analysis.

Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioenergetic, and Regulatory Analyses

Caproate, an important medium-chain fatty acid, can only be synthesized by limited bacterial species by using ethanol, lactate, or certain saccharides. Caproicibacterium lactatifermentans is a promising caproate producer due to its glucose and lactate utilization capabilities. However, the global cellular responses of this bacterium to different carbon sources were not well understood. Here, C. lactatifermentans showed robust growth on glucose but more active caproate synthesis on lactate. Comparative transcriptome revealed that the genes involved in reverse β-oxidation for caproate synthesis and V-type ATPase-dependent ATP generation were upregulated under lactate condition, while several genes responsible for biomass synthesis were upregulated under glucose condition. Based on metabolic pathway reconstructions and bioenergetics analysis, the biomass accumulation on glucose condition may be supported by sufficient supplies of ATP and metabolite intermediates via glycolysis. In contrast, the ATP yield per glucose equivalent from lactate conversion into caproate was only 20% of that from glucose. Thus, the upregulation of the reverse β-oxidation genes may be essential for cell survival under lactate conditions. Furthermore, the remarkably decreased lactate utilization was observed after glucose acclimatization, indicating the negative modulation of lactate utilization by glucose metabolism. Based on the cotranscription of the lactate utilization repressor gene lldR with sugar-specific PTS genes and the opposite expression patterns of lldR and lactate utilization genes, a novel regulatory mechanism of glucose-repressed lactate utilization mediated via lldR was proposed. The results of this study suggested the molecular mechanism underlying differential physiologic and metabolic characteristics of C. lactatifermentans grown on glucose and lactate. IMPORTANCE Caproicibacterium lactatifermentans is a unique and robust caproate-producing bacterium in the family Oscillospiraceae due to its lactate utilization capability, whereas its close relatives such as Caproicibacterium amylolyticum, Caproiciproducens galactitolivorans, and Caproicibacter fermentans cannot utilize lactate but produce lactate as the main fermentation end product. Moreover, C. lactatifermentans can also utilize several saccharides such as glucose and maltose. Although the metabolic versatility of the bacterium makes it to be a promising industrial caproate producer, the cellular responses of C. lactatifermentans to different carbon sources were unknown. Here, the molecular mechanisms of biomass synthesis supported by glucose utilization and the cell survival supported by lactate utilization were revealed. A novel insight into the regulatory machinery in which glucose negatively regulates lactate utilization was proposed. This study provides a valuable basis to control and optimize caproate production, which will contribute to achieving a circular economy and environmental sustainability.

Current Trends in Biological Valorization of Waste-Derived Biomass: The Critical Role of VFAs to Fuel A Biorefinery

The looming climate and energy crises, exacerbated by increased waste generation, are driving research and development of sustainable resource management systems. Research suggests that organic materials, such as food waste, grass, and manure, have potential for biotransformation into a range of products, including: high-value volatile fatty acids (VFAs); various carboxylic acids; bioenergy; and bioplastics. Valorizing these organic residues would additionally reduce the increasing burden on waste management systems. Here, we review the valorization potential of various sustainably sourced feedstocks, particularly food wastes and agricultural and animal residues. Such feedstocks are often micro-organism-rich and well-suited to mixed culture fermentations. Additionally, we touch on the technologies, mainly biological systems including anaerobic digestion, that are being developed for this purpose. In particular, we provide a synthesis of VFA recovery techniques, which remain a significant technological barrier. Furthermore, we highlight a range of challenges and opportunities which will continue to drive research and discovery within the field. Analysis of the literature reveals growing interest in the development of a circular bioeconomy, built upon a biorefinery framework, which utilizes biogenic VFAs for chemical, material, and energy applications.

Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review

Acidogenic fermentation of food waste using mixed microbial cultures can produce carboxylates [or volatile fatty acids (VFA)] as high-valued bioproducts via a complex interplay of microorganisms during different stages of this process. However, the present fermentation systems are incapable of reaching the industrially relevant VFA production yields of ≥50 g/L primarly due to the complex process operation, competitive metabolic pathways, and limited understanding of microbial interplays. Recent reports have demonstrated the significant roles played by microbial communities from different phyla, which work together to control the process kinetics of various stages underlying acidogenic fermentation. In order to fully delineate the abundance, structure, and functionality of these microbial communities, next-generation high-throughput meta-omics technologies are required. In this article, we review the potential of metagenomics and metatranscriptomics approaches to enable microbial community engineering. Specifically, a deeper analysis of taxonomic relationships, shifts in microbial communities, and differences in the genetic expression of key pathway enzymes under varying operational and environmental parameters of acidogenic fermentation could lead to the identification of species-level functionalities for both cultivable and non-cultivable microbial fractions. Furthermore, it could also be used for successful gene sequence-guided microbial isolation and consortium development for bioaugmentation to allow VFA production with high concentrations and purity. Such highly controlled and engineered microbial systems could pave the way for tailored and high-yielding VFA synthesis, thereby creating a petrochemically competitive waste-to-value chain and promoting the circular bioeconomy.Research HighlightsMixed microbial mediated acidogenic fermentation of food waste.Metagenomics and metatranscriptomics based microbial community analysis.Omics derived function-associated microbial isolation and consortium engineering.High-valued sustainable carboxylate bio-products, i.e. volatile fatty acids.

Produce individual medium chain carboxylic acids (MCCA) from swine manure: Performance evaluation and economic analysis

Environmental issues caused by untreated animal manure require the development of resource recovery from waste through a circular economy approach. Producing medium chain carboxylic acids (MCCA) with higher value than biogas from manure has become promising. The objective of this study was to develop an effective individual MCCA produce process utilizing manure. In this study, animal manure was firstly anaerobic fermentation into short chain fatty acids (SCFA), then acidified manure and ethanol were fed into the chain elongation reactor with gradually increasing the organic loading rate (OLR) from 7.0 to 18.5 gCOD/L/d, and the mixed MCCA was separated individually via a fractional distillation process. The SCFA fermentation occurred mainly at the first 10 days, and the optimum concentrations of SCFA for treatments at 2 %VS, 4 %VS and 6 %VS were 6.58, 10.40 and 14.10 g/L, respectively. For the chain elongation reactor, the maximum concentrations of n-caproate and n-caprylate were 10.25 and 0.63 g/L, respectively, which were comparable with that obtained from other complex wastes. Over 90% MCCA can be recovered from the fermentation broth via the optimized extractant of methyl tert-butyl ether (MTBE) and the fractional distillation system. Preliminary economic analysis shows that this MCCA production process presented a higher economic benefit (9.25 $/m³ manure) than traditional biogas production (2.65 $/m³ manure), making MCCA production from swine manure economically competitive. This work provides a new route for manure resource recovery besides the biogas process.

Electro-fermentation: Sustainable bioproductions steered by electricity

The market of biobased products obtainable via fermentation processes is steadily increasing over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC) whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a mean to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying the EF process are still largely unknown. This review paper provides a comprehensive overview of recent literature studies including both AEF and CEF examples with either pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.

The Measurement, Application and Effect of Oxygen in Microbial Fermentations: Focusing on Methane and Carboxylate Production

Oxygen is considered detrimental to anaerobic fermentation processes by many practitioners. However, deliberate oxygen sparging has been used successfully for decades to remove H2S in anaerobic digestion (AD) systems. Moreover, microaeration techniques during AD have shown that small doses of oxygen may enhance process performance and promote the in situ degradation of recalcitrant compounds. However, existing oxygen dosing techniques are imprecise, which has led to inconsistent results between studies. At the same time, real-time oxygen fluxes cannot be reliably quantified due to the complexity of most bioreactor systems. Thus, there is a pressing need for robust monitoring and process control in applications where oxygen serves as an operating parameter or an experimental variable. This review summarizes and evaluates the available methodologies for oxygen measurement and dosing as they pertain to anaerobic microbiomes. The historical use of (micro-)aeration in anaerobic digestion and its potential role in other anaerobic fermentation processes are critiqued in detail. This critique also provides insights into the effects of oxygen on these microbiomes. Our assessment suggests that oxygen dosing, when implemented in a controlled and quantifiable manner, could serve as an effective tool for bioprocess engineers to further manipulate anaerobic microbiomes for either bioenergy or biochemical production.

Recovery Techniques Enabling Circular Chemistry from Wastewater

In an era where it becomes less and less accepted to just send waste to landfills and release wastewater into the environment without treatment, numerous initiatives are pursued to facilitate chemical production from waste. This includes microbial conversions of waste in digesters, and with this type of approach, a variety of chemicals can be produced. Typical for digestion systems is that the products are present only in (very) dilute amounts. For such productions to be technically and economically interesting to pursue, it is of key importance that effective product recovery strategies are being developed. In this review, we focus on the recovery of biologically produced carboxylic acids, including volatile fatty acids (VFAs), medium-chain carboxylic acids (MCCAs), long-chain dicarboxylic acids (LCDAs) being directly produced by microorganisms, and indirectly produced unsaturated short-chain acids (USCA), as well as polymers. Key recovery techniques for carboxylic acids in solution include liquid-liquid extraction, adsorption, and membrane separations. The route toward USCA is discussed, including their production by thermal treatment of intracellular polyhydroxyalkanoates (PHA) polymers and the downstream separations. Polymers included in this review are extracellular polymeric substances (EPS). Strategies for fractionation of the different fractions of EPS are discussed, aiming at the valorization of both polysaccharides and proteins. It is concluded that several separation strategies have the potential to further develop the wastewater valorization chains.

Upgrading the value of anaerobic fermentation via renewable chemicals production: A sustainable integration for circular bioeconomy

The single bioprocess approach has certain limitations in terms of process efficiency, product synthesis, and effective resource utilization. Integrated or combined bioprocessing maximizes resource recovery and creates a novel platform to establish sustainable biorefineries. Anaerobic fermentation (AF) is a well-established process for the transformation of organic waste into biogas; conversely, biogas CO₂ separation is a challenging and expensive process. Biological fixation of CO₂ for succinic acid (SA) mitigates CO₂ separation issues and produces commercially important renewable chemicals. Additionally, utilizing digestate rich in volatile fatty acid (VFA) to produce medium-chain fatty acids (MCFAs) creates a novel integrated platform by utilizing residual organic metabolites. The present review encapsulates the advantages and limitations of AF along with biogas CO₂ fixation for SA and digestate rich in VFA utilization for MCFA in a closed-loop approach. Biomethane and biohydrogen processes CO₂ utilization for SA production is cohesively deliberated along with the role of biohydrogen as an alternative reducing agent to augment SA yields. Similarly, MCFA production using VFA as a substrate and functional role of electron donors namely ethanol, lactate, and hydrogen are comprehensively discussed. A road map to establish the fermentative biorefinery approach in the framework of AF integrated sustainable bioprocess development is deliberated along with limitations and factors influencing for techno-economic analysis. The discussed integrated approach significantly contributes to promote the circular bioeconomy by establishing carbon-neutral processes in accord with sustainable development goals.

Chain elongation process for caproate production using lactate as electron donor in Megasphaera hexanoica

Megasphaera hexnaoica is anaerobic bacteria who has well running reverse β-oxidation pathway. In previous study, the strain showed excellent production of medium chain carboxylic acids (MCCAs) using fructose as electron donor. In this study, chain elongation process study using lactate instead of fructose was conducted in M. hexnaoica fermentation. It was found that M. hexanoica can use lactate as electron donor in chain elongation process. 8.9 g/L caproate production was achieved in fermentation using lactate as sole electron donor. Compare to fructose condition, lactate as electron donor showed more than 3 times higher specific titer and specific productivity. In addition, when fructose and lactate were used as electron donor simultaneously, further improvement of MCCAs production was observed to achieve maximum caproate productivity of 20.9 g/L/day. Utilization of lactate as electron donor in M. hexanoica showed potential opportunity in chain elongation process.

Effect of external acetate on lactate-based carboxylate platform: Shifted lactate overloading limit and hydrogen co-production

Chain elongation is an anaerobic biotechnological process that converts short chain carboxylates and an electron donor (e.g. ethanol, lactate) into more valuable medium chain carboxylates. Caproate production in lactate-based chain elongation is gaining popularity, however, the relation between lactate (electron donor) and acetate (electron acceptor) has not yet been fully elucidated. Herein, for the first time, the effect of an external acetate on the lactate-based chain elongation in a continuously-fed bioreactor was tested to verify how the external acetate would affect the product spectrum, gas production, as well as stability and efficiency of carboxylates production. Periodic fluctuations in caproate production were observed in bioreactor continuously fed with lactate as a sole carbon source due to the lack of an electron acceptor (acetate) and low chain elongation performance. The recovery of stable caproate production (68.9 ± 2.2 mmol C/L/d), total lactate consumption, and high hydrogen co-production (748 ± 76 mL_H2/d) was observed as an effect of the addition of an external acetate. The lactate conversion with the external acetate in the second bioreactor ensured stable and dominant caproate production from the beginning of the process. Moreover, despite the continuous lactate overloading in the process with external acetate, stable caproate production was achieved (71.7 ± 2.4 mmol C/L/d) and previously unobserved hydrogen production occurred (213 ± 30 mL_H2/d). Thus, external electron acceptor addition (i.e. acetate) was proposed as an effective method for stable lactate-based caproate production. Microbiological analysis showed the dominance of microbes closely related to Ruminococcaceae bacterium CPB6 and Acinetobacter throughout the process. Co-occurrence networks based on taxon abundances and process parameters revealed microbial sub-networks responding to lactate concentrations.

Production of n-caproate using food waste through thermophilic fermentation without addition of external electron donors

The effectiveness of producing n-caproate from food waste without external electron donors (EDs) was investigated through batch and semi-continuous fermentation. The maximum concentration of n-caproate reached 10,226.28 mg COD/L during semi-continuous fermentation. The specificity for n-caproate was the highest at 40.19 ± 3.95%, and the soluble COD conversion rate of n-caproate reached up to 22.50 ± 1.09% at the end of batch fermentation. The production of n-caproate was coupled with the generation of lactate as an ED to facilitate chain elongation reactions. When lactate was used as the only substrate, n-butyrate (64.12 ± 20.11%) markedly dominated the products, instead of n-caproate (0.63 ± 0.07%). Microbial community analysis revealed that Caproiciproducens, Rummeliibacillus, and Clostridium_sensu_stricto_12 were the key genera related to n-caproate production. In addition to n-caproate, n-butyrate dominated the products in batch and semi-continuous fermentation with a maximum specificity of 47.59 ± 3.39%. Clostridium_sensu_stricto_7 was committed to producing n-butyrate from lactate.

Butyrate production and purification by combining dry fermentation of food waste with a microbial fuel cell

This study developed and evaluated a high-purity butyrate producing bioprocess from food waste by combining dry fermentation (DF) with a microbial fuel cell (MFC). Acclimatization of a DF reactor with an enrichment culture resulted in high food waste degradation (VS removed, %) and butyrate production. A high VS degradation of 81%, butyrate concentration of up to 24 gCOD_butyrate/L and butyrate yields of 497 gCOD_butyrate/kg VS_added was obtained in the DF reactor. As a result, butyrate comprised 83% of all short chain fatty acids (SCFA) in the DF broth. Acetate (10%) and propionate (7%) comprised the rest of the SCFA. The butyrate composition was further purified by feeding the DF broth to a multi-electrode MFC enriched with anode respiring bacteria (ARB) such as Geobacter sp. (>55%). The ARB in the MFC removed acetate and propionate while purified butyrate was recovered in the MFC effluent. Butyrate purity in the MFC effluent reached as high as 99% at hydraulic retention time of 72 h. Along with butyrate purification, the MFC produced electric power in a range of 0.1-0.6 Wh/gCODbutyrate_recovered (or 0.01-7.85 kWh/ton of food waste), demonstrating that MFCs can be an energy-positive butyrate purification bioprocess.

Opportunities and challenges in microbial medium chain fatty acids production from waste biomass

Medium chain fatty acids (MCFAs) that produced from affordable waste biomass via chain elongation (CE) technology are recognized as the potential alternatives to part fossil-derived chemicals, contributing to the sustainable development of economy and environment. The purpose of this review is to provide comprehensive analyses on the opportunities and challenges of MCFAs production and application. First, both two microbial MCFAs synthesis pathways of reverse β-oxidation and fatty acid biosynthesis were introduced/compared in detail to give readers a thorough understanding of the CE process, with the expectation of further boosting MCFAs production by well distinguishing them. Furthermore, the six key MCFAs production bottlenecks, corresponding research progresses, and possible solutions were analyzed. Five major MCFAs production strategies with their production mechanism, performances, and characteristics were also critically assessed. Additionally, the commercial production status was introduced, and future alternative production mode and research priorities were also recommended.

Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H₂/CO₂. Two stirred tank reactors and two bubble column reactors were operated with H₂/CO₂ gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O₂ L⁻¹ d⁻¹, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH₄ was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O₂ concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O₂ below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L⁻¹ d⁻¹ depending on the reactor (control reactors 0.1–0.8 mmol L⁻¹ d⁻¹). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H₂ availability was high. After air contamination stopped completely, production of n-caproate and CH₄ recovered, with n-caproate production rates of 1.4–1.8 mmol L⁻¹ d⁻¹ (control 0.7–2.1 mmol L⁻¹ d⁻¹). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.

On the nanoscopic structural heterogeneity of liquid n-alkyl carboxylic acids

Herein we report the first in-depth structural characterisation of simple linear carboxylic acids with alkyl tail length ranging from one to six carbon atoms. By means of the SWAXS technique, a pronounced nanoscopic heterogeneity evolving along the aliphatic portion of the molecule is highlighted. Via classical molecular dynamics, the origin of such heterogeneity is unambiguously assigned to the existence of aliphatic domains resulting from the self-segregation of the polar and apolar portions of the molecules. Furthermore, the structural correlation of aliphatic-separated polar domains is responsible for observing the so-called "pre-peak" in the SAXS region.

Bioaugmented Mixed Culture by Clostridium aceticum to Manipulate Volatile Fatty Acids Composition From the Fermentation of Cheese Production Wastewater

Production of targeted volatile fatty acid (VFA) composition by fermentation is a promising approach for upstream and post-stream VFA applications. In the current study, the bioaugmented mixed microbial culture by Clostridium aceticum was used to produce an acetic acid dominant VFA mixture. For this purpose, anaerobic sequencing batch reactors (bioaugmented and control) were operated under pH 10 and fed by cheese processing wastewater. The efficiency and stability of the bioaugmentation strategy were monitored using the production and composition of VFA, the quantity of C. aceticum (by qPCR), and bacterial community profile (16S rRNA Illumina Sequencing). The bioaugmented mixed culture significantly increased acetic acid concentration in the VFA mixture (from 1170 ± 18 to 122 ± 9 mgCOD/L) compared to the control reactor. Furthermore, the total VFA production (from 1254 ± 11 to 5493 ± 36 mgCOD/L) was also enhanced. Nevertheless, the bioaugmentation could not shift the propionic acid dominancy in the VFA mixture. The most significant effect of bioaugmentation on the bacterial community profile was seen in the relative abundance of the Thermoanaerobacterales Family III. Incertae sedis, its relative abundance increased simultaneously with the gene copy number of C. aceticum during bioaugmentation. These results suggest that there might be a syntropy between species of Thermoanaerobacterales Family III. Incertae sedis and C. aceticum. The cycle analysis showed that 6 h (instead of 24 h) was adequate retention time to achieve the same acetic acid and total VFA production efficiency. Biobased acetic acid production is widely applicable and economically competitive with petroleum-based production, and this study has the potential to enable a new approach as produced acetic acid dominant VFA can replace external carbon sources for different processes (such as denitrification) in WWTPs. In this way, the higher treatment efficiency for WWTPs can be obtained by recovered substrate from the waste streams that promote a circular economy approach.

Open Culture Ethanol-Based Chain Elongation to Form Medium Chain Branched Carboxylates and Alcohols

Chain elongation fermentation allows for the synthesis of biobased chemicals from complex organic residue streams. To expand the product spectrum of chain elongation technology and its application range we investigated 1) how to increase selectivity towards branched chain elongation and 2) whether alternative branched carboxylates such as branched valerates can be used as electron acceptors. Elongation of isobutyrate elongation towards 4-methyl-pentanoate was achieved with a selectivity of 27% (of total products, based on carbon atoms) in a continuous system that operated under CO₂ and acetate limited conditions. Increasing the CO₂ load led to more in situ acetate formation that increased overall chain elongation rate but decreased the selectivity of branched chain elongation. A part of this acetate formation was related to direct ethanol oxidation that seemed to be thermodynamically coupled to hydrogenotrophic carboxylate reduction to corresponding alcohols. Several alcohols including isobutanol and n-hexanol were formed. The microbiome from the continuous reactor was also able to form small amounts of 5-methyl-hexanoate likely from 3-methyl-butanoate and ethanol as substrate in batch experiments. The highest achieved concentration of isoheptanoate was 6.4 ± 0.9 mM Carbon, or 118 ± 17 mg/L, which contributed for 7% to the total amount of products (based on carbon atoms). The formation of isoheptanoate was dependent on the isoform of branched valerate. With 3-methyl-butanoate as substrate 5-methylhexanoate was formed, whereas a racemic mixture of L/D 2-methyl-butanoate did not lead to an elongated product. When isobutyrate and isovalerate were added simultaneously as substrates there was a large preference for elongation of isobutyrate over isovalerate. Overall, this work showed that chain elongation microbiomes can be further adapted with supplement of branched-electron acceptors towards the formation of iso-caproate and iso-heptanoate as well as that longer chain alcohol formation can be stimulated.

Potential Valorization of Organic Waste Streams to Valuable Organic Acids through Microbial Conversion: A South African Case Study

The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates the development of technologies that utilize sustainable feedstocks, have simple and robust operations, are feasible at small scale and produce a variety of valuable bioproducts, thus fitting the biorefinery concept. This case study focuses on the microbial production of higher-value products from selected organic waste streams abundant in the South African agricultural sector using microbes adapted to utilize different parts of biomass waste streams. A ruminant-based carboxylate platform based on mixed or undefined anaerobic co-cultures of rumen microorganisms can convert the carbohydrate polymers in the lignocellulosic part of organic waste streams to carboxylic acids that can be upgraded to biofuels or green chemicals. Furthermore, yeast and fungi can convert the simpler carbohydrates (such as the sugars and malic acid in grape and apple pomace) to ethanol and high-value carboxylic acids, such as lactic, fumaric, succinic and citric acid. This review will discuss the combinational use of the ruminal carboxylate platform and native or recombinant yeasts to valorize biomass waste streams through the production of higher-value organic acids with various applications.

Microbial Chain Elongation and Subsequent Fermentation of Elongated Carboxylates as H2-Producing Processes for Sustained Reductive Dechlorination of Chlorinated Ethenes

In situ anaerobic groundwater bioremediation of trichloroethene (TCE) to nontoxic ethene is contingent on organohalide-respiring Dehalococcoidia, the most common strictly hydrogenotrophic Dehalococcoides mccartyi (D. mccartyi). The H₂ requirement for D. mccartyi is fulfilled by adding various organic substrates (e.g., lactate, emulsified vegetable oil, and glucose/molasses), which require fermenting microorganisms to convert them to H₂. The net flux of H₂ is a crucial controlling parameter in the efficacy of bioremediation. H₂ consumption by competing microorganisms (e.g., methanogens and homoacetogens) can diminish the rates of reductive dechlorination or stall the process altogether. Furthermore, some fermentation pathways do not produce H₂ or having H₂ as a product is not always thermodynamically favorable under environmental conditions. Here, we report on a novel application of microbial chain elongation as a H₂-producing process for reductive dechlorination. In soil microcosms bioaugmented with dechlorinating and chain-elongating enrichment cultures, near stoichiometric conversion of TCE (0.07 ± 0.01, 0.60 ± 0.03, and 1.50 ± 0.20 mmol L^-1 added sequentially) to ethene was achieved when initially stimulated by chain elongation of acetate and ethanol. Chain elongation initiated reductive dechlorination by liberating H₂ in the conversion of acetate and ethanol to butyrate and caproate. Syntrophic fermentation of butyrate, a chain-elongation product, to H₂ and acetate further sustained the reductive dechlorination activity. Methanogenesis was limited during TCE dechlorination in soil microcosms and absent in transfer cultures fed with chain-elongation substrates. This study provides critical fundamental knowledge toward the feasibility of chlorinated solvent bioremediation based on microbial chain elongation.

The occurrence and ecology of microbial chain elongation of carboxylates in soils

Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.

Nano zero-valent iron: A pH buffer, electron donor and activator for chain elongation

Chain elongation produce medium chain carboxylates, which are important precursors to many pharmaceuticals, antimicrobials and biofuels. Results in the presented investigations show that the supply of nano zero-valent iron (NZVI) can enhance caproate production. The highest caproate concentration achieved amounted to 27.2 mmol/L when 5 g/L NZVI were added, which was about 100% higher than the control. The study also showed increase of ethanol oxidation and decrease of butyrate and butanol with NZVI addition. Mechanism study showed NZVI can stimulate caproate production by preventing pH to fall below 5.4 through displacement reaction. Electron balance analysis displayed that NZVI provides extra electron by promoting ethanol oxidation and its dissolution. H₂ was the potential electron shuttle between NZVI and chain elongators; High throughput sequencing showed function of NZVI on reshaping of microbial communities, especially enriching Oscillibacter Marseille-P3260, a kind of chain elongator and Corynebacterium which possesses fatty acid biosynthesis and iron utilization.

Selecting fermentation products for food waste valorisation with HRT and OLR as the key operational parameters

Acidogenic fermentation is attractive for food waste valorisation. A better understanding is required on how operation affects product selectivity. This study demonstrated that the hydraulic retention time (HRT) and organic loading rate (OLR) selected fermentation pathways in a single-stage, semi-continuous stirred tank reactor. Three combinations of HRT and OLR were tested to distinguish the effect of each parameter. Three fermentation profiles with distinct microbial communities were obtained. Predominantly n-butyric acid (13 ± 2 gCOD L^-1, 55 ± 14% of carboxylates) was produced at an HRT of 8.5 days and OLR around 12 gCOD L^-1d^-1. Operating at an HRT two days longer, yet with similar OLR, stimulated chain elongation (up to 13.6 gCOD L^-1 of n-caproic acid). This was reflected by a microbial community twice as diverse at longer HRT as indicated by first and second order Hill number (¹D = 24 ± 4, ²D = 12 ± 3) and by a higher relative abundance of genera related to secondary fermentation, such as the VFA-elongating Caproiciproducens spp., and secondary lactic acid fermenter Secundilactobacillus spp.. Operating at a higher OLR (20 gCOD L^-1d^-1) but HRT of 8.5 days, resulted in typical lactic acid fermentation (34 ± 5 gCOD L^-1) harbouring a less diverse community (¹D = 8.0 ± 0.7, ²D = 5.7 ± 0.9) rich in acid-resistant homofermentative Lactobacillus spp. These findings demonstrate that a flexible product portfolio can be achieved by small adjustments in two key operating conditions. This improves the economic potential of acidogenic fermentation for food waste valorisation.

Strategies for optimizing acetyl-CoA formation from glucose in bacteria

Acetyl CoA is an important precursor for various chemicals. We provide a metabolic engineering guideline for the production of acetyl-CoA and other end products from a bacterial chassis. Among 13 pathways that produce acetyl-CoA from glucose, 11 lose carbon in the process, and two do not. The first 11 use the Embden-Meyerhof-Parnas (EMP) pathway to produce redox cofactors and gain or lose ATP. The other two pathways function via phosphoketolase with net consumption of ATP, so they must therefore be combined with one of the 11 glycolytic pathways or auxiliary pathways. Optimization of these pathways can maximize the theoretical acetyl-CoA yield, thereby minimizing the overall cost of subsequent acetyl-CoA-derived molecules. Other strategies for generating hyper-producer strains are also addressed.

Expanding the anaerobic digestion map: A review of intermediates in the digestion of food waste

Anaerobic digestion is a promising technology as a renewable source of energy products, but these products have low economic value and process control is challenging. Identifying intermediates formed throughout the process could enhance understanding and offer opportunities for improved monitoring, control, and valorisation. In this review, intermediates present in the anaerobic digestion process are identified and discussed, including the following: volatile fatty acids, carboxylic acid, amino acids, furans, terpenes and phytochemicals. The key limitations associated with exploiting these intermediates are also addressed including challenging mixed cultures of microbiology, complex feedstocks, and difficult extraction and separation techniques.

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

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

Direct Conversion of Food Waste Extract into Caproate: Metagenomics Assessment of Chain Elongation Process

In a circular economy strategy, waste resources can be used for the biological production of high added-value substances, such as medium chain fatty acids (MCFAs), thus minimising waste and favouring a sustainable process. This study investigates single-stage fermentation processes for the production of MCFAs in a semi-continuous reactor treating the extract of real food waste (FW), without the addition of external electron donors. Two sequential acidogenic fermentation tests were carried out at an organic loading rate (OLR) of 5 and 15 gCOD L⁻¹d⁻¹ with a hydraulic retention time of 4 days and pH controlled at 6 ± 0.2. The highest level of caproate (4.8 g L⁻¹) was observed at OLR of 15 gCOD L⁻¹d⁻¹ with a microbiome mainly composed by lactate-producing Actinomyces, Atopobium, and Olsenella species and caproate-producing Pseudoramibacter. Metagenomic analysis revealed the presence of key enzymes for the production of lactate, such as lactate dehydrogenase and pyruvate ferredoxin oxidoreductase, as well as several enzymes involved in the reverse β-oxidation pathway, thus suggesting the occurrence of a lactate-based chain elongation process.

Potential of medium chain fatty acids production from municipal solid waste leachate: Effect of age and external electron donors

A large quantity of leachate is generated during municipal solid waste collection operation and in landfills due to the large amount of organic waste and high humidity. The content of medium chain fatty acids (MCFAs) in the leachate is a low cost feedstock for bio-based chemical and fuel production processes. The aim of this study is to investigate the MCFA production potential of three leachate ages through chain elongation process under uncontrolled pH batch test. Moreover, the effect of using different external electron donors (ethanol, methanol and a mixture of both) is studied. The experiment consists of characterizing the samples then adding external electron donors with a specific ratio to leachate samples under mesophilic temperature. For this investigation, also a statistical analysis is done, which shows the production of MCFAs is highly influenced by leachate age. The results indicate that the production of even-numbered acids increase from 600 to 1,000 mg/L by the end of the ethanol chain elongation experiment for young leachate. However, a higher MCFA production of more than 1,000 mg/L is achieved by using the mixture of methanol and ethanol as electron donor. Furthermore, all methanol chain elongation experiments lead to an odd-numbered production of MCFAs, such as pentanoic and heptanoic acids. These results confirm the potential improvement of MCFA production from leachate through choosing the optimal leachate age and electron donor. Overall, producing MCFAs from leachate is a good example of circular bio-economy because waste is used to produce biochemicals, which closes the material cycle.

Chain elongators, friends, and foes

Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.

Substrate availability drives mixed culture fermentation of glucose to lactate at steady state

Mixed-culture fermentation (MCF) enables carbon recycling from complex organic waste streams into valuable feedstock chemicals. Using complex microbial consortia, MCF systems can be tuned to produce a range of biochemicals to meet market demand. However, the metabolic mechanisms and community interactions which drive biochemical production changes under differing conditions are currently poorly understood. These mechanisms are critical to useful MCF production models. Furthermore, predictable product transitions are currently limited to pH-driven changes between butyrate and ethanol, and chain-elongation (fed by lactate, acetate, and ethanol) to butyrate, valerate, and hexanoate. Lactate, a high-value biopolymer feedstock chemical, has been observed in transition states, but sustained production has not been described. In this study, steady state lactate production was achieved by increasing the organic loading rate of a butyrate-producing system from limiting to nonlimiting conditions at pH 5.5. Crucially, butyrate production resumed upon return to substrate-limited conditions. 16S ribosomal DNA community profiling combined with metaproteomics demonstrated that the butyrate-producing lineage Megasphaera redirected carbon flow through the methylglyoxal bypass when substrate was nonlimiting, which altered the community structure and metabolic expression toward lactate production. This metabolic mechanism can be included in future MCF models to describe the changes in product generation in substrate nonlimiting conditions.

Effect of ultrasonic pretreatment on chain elongation of saccharified residue from food waste by anaerobic fermentation

Converting biowaste into value-added products has raised the researchers' interests. In this study, bioconversion was applied to produce chain acids from food waste by anaerobic fermentation. To improve the caproic acid production, different pretreatments (i.e., ultrasonic, hydrothermal, and alkaline-thermal) were used for investigating their effects on the acidogenic production and microbial communities. The results showed that ultrasonic and hydrothermal pretreatments (207.8 and 210.1 mg COD/g VS, respectively) were very efficient for enhancing the caproic acid production, compared to the alkaline-thermal pretreated samples and control samples (72.6 and 97.5 mg COD/g VS, respectively). The ultrasonic pretreatment was beneficial for reducing volatile fatty acids (VFAs) during the caproic acid production, resulting in converting more lactic acid to caproic acid by adding the hydrothermal pretreatment. The microbial community analysis showed that the acidogenic bacteria Caproiciproducens dominated the fermentation in this bioconversion process of food waste into chain acids. The Caproiciproducens mainly degraded the proteins and carbohydrates from the saccharified residues of food waste to produce caproic acids through chain elongation procedure. The investigation and optimized method may help develop the bioconversion technology for producing VFAs products from food wastes.

Co-production of hydrogen and caproate for an effective bioprocessing of waste

The objective of the study was to valorize waste stream for the co-production of hydrogen and caproate via open culture fermentation (OCF). Batch studies confirmed that the use of sugar (lactose) together with carboxylates (lactate and acetate) may allow mutual coexistence of chain elongation and dark fermentation processes. During the continuous test in an upflow anaerobic sludge blanket reactor (UASB), acid whey was used as a model feedstock due to a high concentration of lactose and lactate. Shortening hydraulic retention time (HRT) to 2.5 days allowed the co-production of hydrogen and caproate with almost complete methanogenesis inhibition. During the 50 days period, the average hydrogen and caproate production were 1.78 ± 0.75 L_H2/L/d and 133.4 ± 17.9 mmol C/L/d, respectively.