Road to full bioconversion of biowaste to biochemicals centering on chain elongation: A mini review

Research on the conversion of biowaste to MCCAs: A review of recent advances in the electrochemical synergistic anaerobic pathway

Medium-chain carboxylic acids (MCCAs) show great promise as commercial chemicals due to their high energy density, significant product value, and wide range of applications. The production of MCCAs from waste biomass through coupling chain extension with anaerobic fermentation represents a new and innovative approach to biomass utilization. This review provides an overview of the principles of MCCAs production through coupled chain extension and anaerobic fermentation, as well as the extracellular electron transfer pathways and microbiological effects involved. Emphasis is placed on the mechanisms, limitations, and microbial interactions in MCCAs production, elucidating metabolic pathways, potential influencing factors, and the cooperative and competitive relationships among various microorganisms. Additionally, this paper delves into a novel technology for the bio-electrocatalytic generation of MCCAs, which promotes electron transfer through the use of different three-dimensional electrodes, various electrical stimulation methods, and hydrogen-assisted approaches. The insights and conclusions from previous studies, as well as the identification of existing challenges, will be valuable for the further development of high-product-selectivity strategies and environmentally friendly treatments.

Enhanced medium-chain fatty acid production from sewage sludge by combined electro-fermentation and anaerobic fermentation

Electro-fermentation (EF) was combined with anaerobic fermentation (AF) to promote medium-chain fatty acid (MCFA) from sewage sludge. Results showed that EF at acidification process significantly increased short-chain fatty acid (SCFA) production of by 0.5 times (82.4 mmol C/L). AF facilitated the chain elongation (CE) process by enhancing the SCFA conversion. Combined EF at acidification and AF at CE (EF-AF) achieved the highest MCFA production of 27.9 mmol C/L, which was 20 %-866 % higher than the other groups. Electrochemical analyses showed that enhanced SCFA and MCFA production was accompanied with good electrochemical performance at acidification and CE. Microbial analyses showed that EF-AF promoted MCFA production by enriching electrochemically active bacteria (EAB, Bacillus sp.). Enzyme analyses indicated that EF-AF promoted MCFA production by enriching the functional enzymes involved in Acetyl-CoA formation and the fatty acid biosynthesis (FAB) pathway. This study provided new insights into the production of MCFA from enhanced sewage sludge.

Hydrochar and synthetic natural gas co-production for a full circular economy implementation via hydrothermal carbonization and methanation: An economic approach

Herein we study the economic performance of hydrochar and synthetic natural gas co-production from olive tree pruning. The process entails a combination of hydrothermal carbonization and methanation. In a previous work, we evidenced that standalone hydrochar production via HTC results unprofitable. Hence, we propose a step forward on the process design by implementing a methanation, adding value to the gas effluent in an attempt to boost the overall process techno-economic aspects. Three different plant capacities were analyzed (312.5, 625 and 1250 kg/hr). The baseline scenarios showed that, under the current circumstances, our circular economy strategy in unprofitable. An analysis of the revenues shows that hydrochar selling price have a high impact on NPV and subsidies for renewable coal production could help to boost the profitability of the process. On the contrary, the analysis for natural gas prices reveals that prices 8 times higher than the current ones in Spain must be achieved to reach profitability. This seems unlikely even under the presence of a strong subsidy scheme. The costs analysis suggests that a remarkable electricity cost reduction or electricity consumption of the HTC stage could be a potential strategy to reach profitability scenarios. Furthermore, significant reduction of green hydrogen production costs is deemed instrumental to improve the economic performance of the process. These results show the formidable techno-economic challenge that our society faces in the path towards circular economy societies.

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.

Advanced treatment and valorization of food waste through staged fermentation and chain elongation

A novel valorization approach of food waste via staged fermentation and chain elongation was proposed. Food waste was moderately saccharified, saccharification effluent was fermented to produce ethanol and saccharification residue was hydrolyzed and acidified to produce VFAs. The yeast fermentation effluent and hydrolytic acidification effluent were sequentially performed for chain elongation. Ethanol and volatile fatty acids from staged fermentation were suitable for direct chain elongation and the n-caproate production was 184.69 mg COD/g VS when yeast fermentation effluent to hydrolytic acidification effluent ratio was 2:1. Food waste was deeply utilized with an organic conversion of 80%. The relative abundance of Clostridium sensu stricto increased during chain elongation, which might be responsible for the improvement of n-caproate production. A profit of 10.65 USD/t was estimated for chain elongation of food waste staged fermentation effluent. This study provided a new technology to achieve advanced treatment and high-valued utilization of food waste.

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.

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.

Acclimation of anaerobic fermentation microbiome with acetate and ethanol for chain elongation and the biochemical response

Medium chain fatty acids (MCFAs) production is a promising method for resource recovery from organic wastes. In this study, the microbial community structure shift along the long-term acclimation experiment and the concomitant effect of H₂ level on chain elongation performance was investigated. Chain elongation microbiome could be rapidly acclimated from traditional anaerobic fermentation consortia. Genera Caproiciproducens, Clostridium sensu stricto 12, Rummeliibacillus and Oscillibacter was found to be dominant during the operation. The H₂ was accumulated in the headspace by increasing the ethanol input, which inhibited oxidation of caproate and butyrate immediately, while its inhibition effect on chain elongation was delayed. H₂ level in the headspace was positively correlated to the MCFAs production related bacteria. However, too much H₂ accumulated might be suppressive for MCFAs production in the long term. It might result from the thermodynamic barrier for discarding excess reducing equivalents under high H₂ level, which further gave rise to ethanol accumulation in this system.

Regulation of acidogenic fermentation through exogenous additives for promoting carbon conversion of food waste in two-phase anaerobic system

In this study, exogenous Megasphaera elsdenii inoculum and acetate supplementation were introduced at the acidogenic phase to regulate the acidogenic fermentation pathway and assess their effects on food waste (FW) carbon conversion in two-phase anaerobic digestion (AD) system. These two additives significantly accelerated organic removal efficiency and subsequently increased FW hydrolysis and acidogenesis by 16% and 35%, respectively. As expected, two exogenous additives promoted butyrate fermentation during FW acidogenesis. With regard to the role of exogenous additives, both hydrogen and butyrate yields increased by over 60%. This desired increment resulted in a 25% increase in methane production. The overall carbon conversion from FW in the integrated two-phase AD system was enhanced by biochemical additives, which was 1.3-fold higher than that in control without any additives. Collectively, findings demonstrate the feasibility of regulating acidogenic fermentation via exogenous biochemical additives and its benefits on FW carbon conversion during AD process.

Ecology of food waste chain-elongating microbiome

Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L^-1 d^-1 selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.

A preliminary study on the feasibility of industrialization for n-caproic acid recovery from food wastewater: From lab to pilot

Food wastewater is associated with greenhouse gas emission and has a significant water footprint. Here, the platform chemical n-caproate was recovered from liquor brewing wastewater at maximum and mean concentrations of 26.4 g/L and 17.0 ± 4.3 g/L, respectively, after 377 d operation. Laboratory-scale lactate-driven chain elongation (CE) process was implemented first. Taxonomic composition and metagenomic data analyses revealed that Caproiciproducens (e.g., Ruminococcaceae bacterium CPB6) and bacteria affiliated with Lachnospiraceae transformed lactate to n-caproate by reverse β-oxidation and/or fatty acid biosynthesis. The lactate-driven CE process was then scaled up from 2.5 L to 500 L and achieved a n-caproate production of 14.5 ± 0.6 g/L within 96 h. n-Caproic acid was extracted at a concentration and purity of 815.9 ± 8.3 g/L and 88.6 ± 8.9 %, respectively. The present study demonstrated a commercially viable strategy for resource recovery and carbon fixation from food waste streams.

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.

Simultaneous medium chain fatty acids production and process carbon emissions reduction in a continuous-flow reactor: Re-understanding of carbon flow distribution

Due to its wide application and high value, the production of medium chain fatty acids (MCFAs) from waste biomass has become one of the worldwide research hotspots. Increasing the carbon element participation from short-chain fatty acids to the form of MCFAs is also conductive to reduce the release of biogas from biological treatment process, because carbon is in the form of MCFAs instead of biogas which directly contribute to process carbon emissions reduction. However, many barriers limiting MCFAs production and application remain to be resolved. Aiming continuous MCFAs production from lactate-rich waste biomass, this study optimized the operation conditions and clarified the main limiting factors and possible mechanisms. The maximum caproic acid concentration of 2.757 g/L were obtained at the Upflow Velocity (ULV) of 1.15 m/h and pH 4.9-5.1. Caproiciproducens, Pseudoramibacter, norank_f_Eubacteriaceae, and Oscillibacter were identified to be the dominant microbial genus responsible for MCFAs production from lactate. The reduction of carbon emissions calculation was also studied in the present processes.

Efficient production of n-caproate from syngas by a co-culture of Clostridium aceticum and Clostridium kluyveri

In recent years, the possibility of merging technologies for waste recovery such as those based on syngas fermentation and chain elongation has been studied for the production of medium chain fatty acids (MCFAs) and bioalcohols, in an attempt to integrate the concept of circular economy in the industry. Nevertheless, one of the main issues of this approach is the pH mismatch between acetogens and chain elongating microorganisms. This work reports, for the first time, the suitability of a co-culture of C. aceticum and C. kluyveri metabolizing syngas at near neutral pH in stirred tank bioreactors. For this purpose, bioreactor studies were carried out with continuous syngas supply. In the first experiment, maximum concentrations of n-butyrate and n-caproate of 7.0 and 8.2 g/L, respectively, were obtained. In the second experiment, considerable amounts of n-butanol were produced as a result of the reduction, by C. aceticum, of the carboxylates already formed in the broth. In both experiments, ethanol was used as an exogenous electron agent at some point. Finally, batch bottle assays were performed with a pure culture of C. aceticum grown on CO in presence of n-butyrate to assess and confirm its ability to produce n-butanol, reaching concentrations up to 951 mg/L, with a n-butyrate conversion efficiency of 96%, which had never been reported before in this species. Therefore, this work contributes to the state of the art, presenting a novel system for the bioproduction of MCFAs by combining syngas fermentation and chain elongation at near neutral pH, as opposed to the acidic pH range used in all previously reported literature.

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.

Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways

Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.

Biological production of medium-chain carboxylates through chain elongation: An overview

Medium chain carboxylates (MCCs) have wide applications in various industries, but the traditional MCCs production methods are costly and unsustainable. Anaerobic fermentation offers a more scalable, economical and eco-friendly platform for producing MCCs through chain elongation which converts short chain carboxylates and electron donor into more valuable MCCs. However, the underlying microbial pathways are not well understood. In this review, biological production of MCCs through chain elongation is introduced elaborately, including the metabolic pathways, electron donor and substrates, microorganisms and influencing factors. Then, the strategies for enhancing MCCs production are extensively analyzed and summarized, along with the technologies for MCCs separation from the fermentation broth. Finally, challenges and perspectives concerning the large-scale MCCs production are proposed, providing suggestions for the future research. Extensive review demonstrated that anaerobic fermentation has great potential in achieving economical and sustainable MCCs production from complex organic substrates, including organic waste streams, which would significantly broaden the application of MCCs, especially in the renewable energy field. An interdisciplinary approach with knowledge from microbiology and biochemistry to chemical separations and environmental engineering is required to use this promising technology as a valorization method for converting organic biomass or organic wastes into valuable MCCs.

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.

Phenol promoted caproate production via two-stage batch anaerobic fermentation of organic substance with ethanol as electron donor for chain elongation

The conversion of organic wastes/wastewater into medium chain fatty acids (MCFAs) such as caproate has attracted much attention, while the effects of toxic compounds on the process have rarely been studied. The present study investigated the effects of phenol (0-1.5 g/L), which is a toxicant and present in various organic wastes, on the caproate production in the chain elongation (CE) process with ethanol as electron donor via two-stage batch anaerobic fermentation of glucose. The results showed phenol ≤ 1 g/L did not affect short chain fatty acids (SCFAs) production, while 1 g/L phenol increased caproate production by 59.9% in the following CE process. The higher selectivity of caproate and higher consumption of ethanol contributed to the higher caproate production at 1 g/L phenol. It was also shown 1 g/L phenol had more positive effect on CE of butyrate than acetate. 1.5 g/L phenol inhibited both SCFAs production and CE processes. 16S rRNA genes analysis showed phenol had slight effect on the microbial communities for SCFAs production, while it obviously changed the dominant microbes in CE process. For CE process, metagenomic analysis was further conducted and phenol mainly affected fatty acid biosynthesis (FAB) pathway, but not reverse β-oxidization (RBO) pathway. 1 g/L phenol increased the abundances of genes in FAB pathway, which could be related with the higher caproate production. Genome reconstruction identified the dominant microbial species in CE process, which were changed with different concentrations of phenol. Most of the dominant species were new microbial species potentially involved in CE. The syntrophic cooperation between Petrimonas mucosa FDU058 and Methanofollis sp. FDU007 might play important role in increased caproate production at 1 g/L phenol, and their adaption to phenol could be due to the presence of genes relating with active efflux system and refolding of proteins.

Functional genome-centric view of the CO-driven anaerobic microbiome

CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.

A Downstream Processing Cascade for Separation of Caproic and Caprylic Acid from Maize Silage-Based Fermentation Broth

Production of caproic and caprylic acid through anaerobic fermentation of crops or residual and waste biomass has been regarded as an alternative to the conventional ways, where plant oils and animal fats are mostly used. The downstream processing of the fermentation broth is a particular challenge since the broth has a highly complex composition and low concentrations of the target products. In this study, the proof-of-principle for a separation cascade for caproic (C6) and caprylic acid (C8) produced in a maize silage-based fermentation process was demonstrated. For clarification of the fermentation broth, a filter press and a ceramic ultrafiltration membrane was used to remove coarse solids and to separate suspended particles and macromolecules from the fermentation broth, respectively. With both techniques, the dry matter content was reduced from 6.8 to 2.3% and a particle-free product solution was obtained. Subsequently, the carboxylic acids were extracted with oleyl alcohol by liquid-liquid extraction with an extraction efficiency of 85% for C6 and 97% for C8. Over the whole cascade, 58% of caproic acid and 66% of caprylic acid were recovered from the fermentation broth into the extract. Among all separation steps, solid-liquid separation with the filter press caused the major part of the product loss of 21% of each carboxylic acid. By using separation equipment with a better solid separation efficiency such as decanter centrifuges or belt filter presses this loss could be minimized.

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.

Anaerobic digestion of organic waste: Recovery of value-added and inhibitory compounds from liquid fraction of digestate

Anaerobic digestion, as an eco-friendly waste treatment technology, is facing the problem of low stability and low product value. Harvesting value-added products beyond methane and removing the inhibitory compounds will unleash new vitality of anaerobic digestion, which need to be achieved by selective separation of certain compounds. Various methods are reviewed in this study for separating valuable products (volatile fatty acids, medium-chain carboxylic acids, lactic acid) and inhibitory substance (ammonia) from the liquid fraction of digestate, including their performance, applicability, corresponding limitations and roadmaps for improvement. In-situ extraction that allows simultaneous production and extraction is seen as promising approach which carries good potential to overcome the barriers for continuous production. The prospects and challenges of the future development are further analyzed based on in-situ extraction and economics.

Effect of high concentration of ammonium on production of n-caproate: Recovery of a high-value biochemical from food waste via lactate-driven chain elongation

Ammonium accumulation is inevitable during the fermentation of food waste (FW), challenging the application of chain elongation process upgrading FW into the high-value biochemical n-caproate, which is a medium chain carboxylate. This study is the first to investigate ammonium inhibition of lactate-driven chain elongation process. The short-term exposure of a Clostridium IV-dominated chain elongating reactor microbiome at an ammonium concentration of 1-4 g L^-1 linearly decreased n-caproate production by 25-80%. High levels of ammonium (≥5 g L^-1) could cause failure of chain elongation, shifting the product from n-caproate to propionate. The involved mechanisms revealed that ammonium reshaped the microbial community from Clostridium IV domination to Clostridium IV and Propionibacterium co-domination (based on 16S rRNA sequencing) and reduced the activities of key enzymes involved in the reversed β-oxidization pathway. We propose an effective strategy from our study, which is the first one to do in our knowledge, to upgrade raw FW without dilution to n-caproate: lowering the ammonium accumulation to 1.0 g L^-1 at the setup phase for adaptation and prolonging the hydraulic retention time (10 days) during the operation phase for the colonization of chain-elongation bacteria. These findings lay a foundation for the implementation of the LCE process on FW, providing an alternative way to alleviate the global FW crisis.

Microbial Ecological Mechanism for Long-Term Production of High Concentrations of n-Caproate via Lactate-Driven Chain Elongation

Lactate-driven chain elongation (LCE) has emerged as a new biotechnology to upgrade organic waste streams into a valuable biochemical and fuel precursor, medium-chain carboxylate, n-caproate. Considering that a low cost of downstream extraction is critical for biorefinery technology, a high concentration of n-caproate production is very important to improve the scale-up of the LCE process. We report here that in a nonsterile open environment, the n-caproate concentration was increased from the previous record of 25.7 g·liter^-1 to a new high level of 33.7 g·liter^-1 (76.8 g chemical oxygen demand [COD]·liter ^{- 1}), with the highest production rate being 11.5 g·liter^-1·day^-1 (26.2 g COD·liter ^{- 1}·day^-1). In addition, the LCE process remained stable, with an average concentration of n-caproate production of 20.2 ± 5.62 g·liter^-1 (46.1 ± 12.8 g COD·liter ^{- 1}) for 780 days. Dynamic changes in taxonomic composition integrated with metagenomic data reveal the microbial ecology for long-term production of high concentrations of n-caproate: (i) the core microbiome is related to efficient functional groups, such as Ruminococcaceae (with functional strain CPB6); (ii) the core bacteria can maintain stability for long-term operation; (iii) the microbial network has relatively low microbe-microbe interaction strength; and (iv) low relative abundance and variety of competitors. The network structure could be shaped by hydraulic retention time (HRT) over time, and long-term operation at an HRT of 8 days displayed higher efficacy.IMPORTANCE Our research revealed the microbial network of the LCE reactor microbiome for n-caproate production at high concentrations, which will provide a foundation for designing or engineering the LCE reactor microbiome to recover n-caproate from organic waste streams in the future. In addition, the hypothetical model of the reactor microbiome that we proposed may offer guidance for researchers to find the underlying microbial mechanism when they encounter low-efficiency n-caproate production from the LCE process. We anticipate that our research will rapidly advance LCE biotechnology with the goal of promoting the sustainable development of human society.

Inoculum microbiome composition impacts fatty acid product profile from cellulosic feedstock

Conversion of organic wastes to fatty acids rather than methane through anaerobic digestion-based technologies has considerable promise. However, the relationships between microbiome structure and fatty acids produced from cellulosic feedstocks are not well understood. This study investigated the nature of those relationships for anaerobic digester sludge, bison rumen, and cattle rumen inocula grown on cellulose. Acetic acid production was highest in anaerobic sludge reactors, while propionic acid production was highest in cattle rumen reactors. Butyric and pentanoic acid were produced at the highest rates in bison rumen before Day 5. Reactor microbiomes remained distinct, despite identical operating conditions. Novel associations linked Alistipes with butyric acid production and Eubacterium nodatum and Clostridiales bacterium with pentanoic acid production. This study provides new insights into the ability of microbiomes to convert cellulose to different fatty acid mixtures and adds impetus for the rewiring of anaerobic digestion to generate high-value products.

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.

Robust operation through effluent recycling for hydrogen production from the organic fraction of municipal solid waste

The stability of fermentative hydrogen production from the organic fraction of municipal solid waste (OFMSW) was evaluated in this work using a strategy of effluent recycling. Three pretreatment conditions were applied on the recycled effluent: a) no heat shock treatment, b) one initial heat shock treatment (90 °C, 30 min) and c) systematic heat shock treatment at the beginning of each fermentation. When a systematic heat shock was applied, a maximal hydrogen yield of 17.2 ± 3.8 mLH₂/gVS was attained. The hydrogen productivity was improved by 331% reaching a stable value of 1.51 ± 0.29 mLH₂/gVS/h, after 8 cycles of effluent recycling. This strategy caused a sharp decrease of diversity with stable co-dominance of hydrogen- and lactate-producing bacteria, ie. Clostridiales and Lactobacillales, respectively. For the other conditions, a sharp decrease of the hydrogen yields was observed showing the importance of applying a heat shock treatment for optimal hydrogen production with effluent recycling.

Fermentation of Organic Residues to Beneficial Chemicals: A Review of Medium-Chain Fatty Acid Production

Medium-chain fatty acids (MCFAs) have a variety of uses in the production of industrial chemicals, food, and personal care products. These compounds are often produced through palm refining, but recent work has demonstrated that MCFAs can also be produced through the fermentation of complex organic substrates, including organic waste streams. While “chain elongation” offers a renewable platform for producing MCFAs, there are several limitations that need to be addressed before full-scale implementation becomes widespread. Here, we review the history of work on MCFA production by both pure and mixed cultures of fermenting organisms, and the unique metabolic features that lead to MCFA production. We also offer approaches to address the remaining challenges and increase MCFA production from renewable feedstocks.

Adjusting Organic Load as a Strategy to Direct Single-Stage Food Waste Fermentation from Anaerobic Digestion to Chain Elongation

Production of medium chain carboxylic acids (MCCA) as renewable feedstock bio-chemicals, from food waste (FW), requires complicated reactor configurations and supplementation of chemicals to achieve product selectivity. This study evaluated the manipulation of organic loading rate in an un-supplemented, single stage stirred tank reactor to steer an anaerobic digestion (AD) microbiome towards acidogenic fermentation (AF), and thence to chain elongation. Increasing substrate availability by switching to a FW feedstock with a higher COD stimulated chain elongation. The MCCA species n-caproic (10.1 ± 1.7 g L−1) and n-caprylic (2.9 ± 0.8 g L−1) acid were produced at concentrations comparable to more complex reactor set-ups. As a result, of the adjusted operating strategy, a more specialised microbiome developed containing several MCCA-producing bacteria, lactic acid-producing Olsenella spp. and hydrogenotrophic methanogens. By contrast, in an AD reactor that was operated in parallel to produce biogas, the retention times had to be doubled when fed with the high-COD FW to maintain biogas production. The AD microbiome comprised a diverse mixture of hydrolytic and acidogenic bacteria, and acetoclastic methanogens. The results suggest that manipulation of organic loading rate and food-to-microorganism ratio may be used as an operating strategy to direct an AD microbiome towards AF, and to stimulate chain elongation in FW fermentation, using a simple, un-supplemented stirred tank set-up. This outcome provides the opportunity to repurpose existing AD assets operating on food waste for biogas production, to produce potentially higher value MCCA products, via simple manipulation of the feeding strategy.

Role of Microbial Hydrolysis in Anaerobic Digestion

There is a growing need of substrate flexibility for biobased production of energy and value-added products that allows the application of variable biodegradable residues within a circular economy. It can be used to balance fluctuating energy provision of other renewable sources. Hydrolysis presents one of the biggest limitations during anaerobic digestion. Methods to improve it will result in broader process applicability and improved integration into regional material cycles. Recently, one focus of anaerobic digestion research has been directed to systems with a separate hydrolysis–acidogenesis stage as it might be promised to improve process performance. Conditions can be adjusted to each class of microorganisms individually without harming methanogenic microorganisms. Extensive research of separate biomass pretreatment via biological, chemical, physical or mixed methods has been conducted. Nevertheless, several methods lack economic efficiency, have a high environmental impact or focus on specific substrates. Pretreatment via a separate hydrolysis stage as cell-driven biotransformation in a suspension might be an alternative that enables high yields, flexible feeding and production, and a better process control. In this review, we summarize existing technologies for microbial hydrolytic biotransformation in a separate reactor stage and the impacts of substrate, operational parameters, combined methods and process design as well as remaining challenges.

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.

Multispecies microbial communities determine the fate of materials in the environment and can be harnessed to produce beneficial products from renewable resources. In a recent example, fermentations by microbial communities have produced medium-chain fatty acids (MCFAs). Tools to predict, assess, and improve the performance of these communities, however, are limited. To provide such tools, we constructed two metabolic models of MCFA-producing microbial communities based on available genomic, transcriptomic, and metabolomic data. The first model is a unicellular model (iFermCell215), while the second model (iFermGuilds789) separates fermentation activities into functional guilds. Ethanol and lactate are fermentation products known to serve as substrates for MCFA production, while acetate is another common cometabolite during MCFA production. Simulations with iFermCell215 predict that low molar ratios of acetate to ethanol favor MCFA production, whereas the products of lactate and acetate coutilization are less dependent on the acetate-to-lactate ratio. In simulations of an MCFA-producing community fed a complex organic mixture derived from lignocellulose, iFermGuilds789 predicted that lactate was an extracellular cometabolite that served as a substrate for butyrate (C4) production. Extracellular hexanoic (C6) and octanoic (C8) acids were predicted by iFermGuilds789 to be from community members that directly metabolize sugars. Modeling results provide several hypotheses that can improve our understanding of microbial roles in an MCFA-producing microbiome and inform strategies to increase MCFA production. Further, these models represent novel tools for exploring the role of mixed microbial communities in carbon recycling in the environment, as well as in beneficial reuse of organic residues.

IMPORTANCE Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.

Landfill site selection using multi criteria decision making: Influential factors for comparing locations

Although a lot of research has focused on energy recovery and recycling of valuable materials from wastes to reduce loads on landfills, landfilling is still an inseparable part of solid waste management. Since landfills potentially pose a risk to human health and the surrounding environment, landfill site selection is an important endeavor that has to be carried out with great care. Choosing a suitable location for landfills depends on several factors and is a complicated procedure. In this paper, a comprehensive review of landfill site selection methods, with an emphasis on multi criteria decision making (multiple criteria decision analysis) has been presented. Assessments indicate that the most frequently used methods are weighted linear combination (WLC), ordered weighted averaging (OWA), analytic hierarchy process (AHP), fuzzy analytic hierarchy process (F-AHP), TODIM, fuzzy TODIM, analytic network process (ANP), fuzzy-analytic network process (F-ANP), and grey systems theory, each of which is discussed. The most widely used factors for selecting a landfill site are groundwater depth, surface water vicinity, elevation, land slope, soil permeability, soil stability, flooding susceptibility, lithology and stratification, faults, land use type, nearby settlements and urbanization, cultural and protected site vicinity, wind direction, roads, railways, proximity to building materials, pipelines and powerlines, and proximity to airports.

Kinetic modeling of anaerobic carboxylic acid production from swine wastewater

This work aimed to evaluate the potential of anaerobic carboxylic acids (CA) production from swine wastewater (SW), perform modeling studies of the acidogenic process and estimate the kinetic parameters. Tests were carried out in four batch reactors with 250 mL reaction volume, with brewery sludge as inoculum and using chloroform (0.05%, v/v) for methanogenesis inhibition. Hydrolysis was the main limiting step of CA production from SW, once that it took more than twenty days for the particulate COD consumption to stabilize and fourteen days to produce 60% of the acids formed. A yield of 0.33 mg mgCOD_A^-1, corresponding to 0.40 mgCOD mgCOD_A^-1, was obtained. Kinetic models describing logistic growth functions were best suited to simulate CA production.

Protein surface engineering of endoglucanase Penicillium verruculosum for improvement in thermostability and stability in the presence of 1-butyl-3-methylimidazolium chloride ionic liquid

Thermostability and stability in ionic liquids are essential properties of cellulases that are applied in industrial processes of bioconversion. Engineering of protein surface of endoglucanase II from Penicillium verruculosum was used to improve the enzyme thermostability and stability in 1-butyl-3-methylimidazolium chloride ([Bmim]Cl). The engineering was based on analysis of the protein surface topography and enhanced by multiple sequence alignment and ΔΔG calculations. In the case of the thermostability, half-life time was improved in 1.3-1.6 times at 70 °C and 1.2-1.4 times at 80 °C. In the case of the stability in [Bmim]Cl, the residual activity after 72 h of incubation in the presence of [Bmim]Cl (50 g/L, 50 °C, pH 4.5) was 1.7-1.9 times greater for the tailored enzyme. The yield of reducing sugars after enzymatic hydrolysis of aspen wood pretreated with [Bmim]Cl was 10-20% higher with the tailored endoglucanase.