Enhancing electron transfer efficiency in microbial electrochemical systems for bioelectricity and chemical production

Microbial electrochemical systems have emerged as promising platforms for chemical production and bioelectricity generation by utilizing cost-effective substrates. However, their performance is limited by the efficiency of both intracellular and extracellular electron transfer. This review systematically summarizes strategies to enhance electron transfer from a microbial perspective, including improvements in extracellular electron transfer, intracellular electron regeneration, and the establishment of electroactive microbial consortia. In addition, the working mechanisms and limitations of these strategies are analyzed. Furthermore, the potential applications of microbial electrochemical systems in bioelectricity production, chemical synthesis, and industrial-scale applications are explored. Finally, the current challenges of microbial electrochemical systems are discussed, and potential solutions are proposed to advance their practical applications.

One-Pot lignin bioconversion to polyhydroxyalkanoates based on hierarchical utilization of heterogeneous compounds

Pseudomonas putida degraded 35 % of compounds in alkali-pretreated lignin liquor under nitrogen-replete conditions but with low polyhydroxyalkanoates (PHA) production, while limiting nitrogen supplement improved PHA content (PHA/dry cell weight) to 43 % at the expense of decreased lignin degradation of 22 %. Increase of initial cell biomass (0.1-1.5 g/L) monotonically improved the lignin degradation from 22 % to 33 % under nitrogen-limited conditions. Hierarchical utilization of heterogenous compounds under cell growth restricted conditions has been unveiled - simple carbon sources were prioritized for valorization, followed by aromatic compounds bioconversion. Based on the results of hierarchy and leveraging the initial bacterial biomass, acetate was augmented to facilitate one-pot lignin bioconversion under nitrogen-limited conditions. This approach improved lignin bioconversion closer to its upper degradation limit of 35 %, concomitant with PHA yield of 39 mg/g-lignin. Anaerobic digestion of lignocellulose was redesigned to favor acetate-type fermentation, with acetate constituting 91 wt%, providing an economic source of acetate.

Engineering microbial metabolic homeostasis for chemicals production

Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.

Targeted volatile fatty acid production based on lactate platform in mixed culture fermentation: Insights into carbon conversion and microbial metabolic traits

In this study, the effects of fermentation pH and redox potential on the performance of the lactate platform were comprehensively evaluated. The results indicated that the type of acidogenic fermentation was influenced by redox potential, while pH was correlated with volatile fatty acid yield. The highest propionate yield was achieved under anaerobic conditions at a pH of9, with the dominant genus Serpentinicella producing propionate through the acrylate pathway. The highest acetate yield was produced under facultative conditions at a pH of 6. This production was primarily facilitated by the dominant genera unclassified_f__Enterobacteriaceae and Desulfovibrio, which exhibited significant upregulation of the expression of related genes. Furthermore, ecological processes were employed to establish the relationship between environmental factors and microbial communities. This study emphasized the process of converting lactate into volatile fatty acid, providing a theoretical basis for future strategies aimed at regulating targeted acid production.

Towards microbial consortia in fermented foods for metabolic engineering and synthetic biology

The fermented foods microbiota, whose community structures evolve through a succession of different microbial groups, play a central role in fermented food production. The texture and flavor, functions, shelf-life and safety, are largely determined by the interactions among bacteria and yeast within these communities. Although much indispensable work has described the microbial composition and succession in various fermentation foods, yet the specific microbial interactions involved are not well understood. Here, we review the current mechanisms of microbial interactions (amensalism, competition, commensalism, and mutualism) existed in the fermented foods. We also examine the function of these interactions. In addition, we provide our perspectives on the future development of functional and novel fermented foods by combining the new starter cultures with the native microbial consortia and applications of these stable and robust microbial consortia for metabolic engineering and synthetic biology.

Improved volatile fatty acid production in anaerobic digestion via simultaneous temperature regulation and persulfate activation by biochar: Chemical and biological response mechanisms

Increasing volatile fatty acid (VFA) production via persulfate activation (i.e., chemical effect) in anaerobic digestion (AD) is an emerging resource utilization method. However, the reaction mechanisms responsible for improving VFA production in AD via simultaneous temperature regulation and persulfate activation by biochar remain unclear. In this study, three PB15 treatment systems of low temperature (15 °C), medium temperature (35 °C) and high temperature (55 °C) were set to explore the relationship between VFAs production and treatment temperature and the influence of temperature on the reaction mechanism. The results show that the improvement of hydrolysis and acidification efficiency of the system in the medium temperature system is the highest. The VFA yield and acid production rate in the treatment group at 35 °C were 2.49 and 5.22 times higher than those in the control group, respectively. The chemical effect effectively initiated the anaerobic acid production process and maintained the dominant role of the biological effect. The activity of persulfate is too low at low temperature, and its decomposition is too fast at high temperature. Plenty of free radicals lead to enhanced oxidation of the system, which may kill the fermentation bacteria. The NCM model indicates that microbial stability is reduced in high temperature systems. The SEM model showed that temperature change mainly affected substrate degradation by hydrolytic bacteria and indirectly affected acid production by acid-producing bacteria. This study provides a new strategy for realizing pollutant recycling and increasing VFAs production in cold area.

Advances and prospects for lactic acid production from lignocellulose

Lactic acid is a versatile building block that can be produced via microbial fermentation. Owing to the high optical purity, approximately 90 % of lactic acid is produced by microbes. Recently, the biosynthesis of lactic acid from lignocellulose has concerned much attentions. However, the cost-effective process faces several obstacles because of the complex structure of lignocellulose. This review will comprehensively summarize the state-of-the-art lactic acid production from lignocellulose, including the commonly used lactate-producing microorganisms, the co-utilization of glucose and xylose for the lactic acid production, as well as the lactic acid production from lignocellulose hydrolysate. Furthermore, the strategies regarding the lignocellulosic lactic acid production via consolidated bioprocessing will be also discussed, which can greatly reduce the complexity of the fermentation process.

Strategies and tools to construct stable and efficient artificial coculture systems as biosynthetic platforms for biomass conversion

Inspired by the natural symbiotic relationships between diverse microbial members, researchers recently focused on modifying microbial chassis to create artificial coculture systems using synthetic biology tools. An increasing number of scientists are now exploring these systems as innovative biosynthetic platforms for biomass conversion. While significant advancements have been achieved, challenges remain in maintaining the stability and productivity of these systems. Sustaining an optimal population ratio over a long time period and balancing anabolism and catabolism during cultivation have proven difficult. Key issues, such as competitive or antagonistic relationships between microbial members, as well as metabolic imbalances and maladaptation, are critical factors affecting the stability and productivity of artificial coculture systems. In this article, we critically review current strategies and methods for improving the stability and productivity of these systems, with a focus on recent progress in biomass conversion. We also provide insights into future research directions, laying the groundwork for further development of artificial coculture biosynthetic platforms.

Biofilm application for anaerobic digestion: a systematic review and an industrial scale case

Biofilm is a syntrophic community of microorganisms enveloped by extracellular polymeric substances and displays remarkable adaptability to dynamic environments. Implementing biofilm in anaerobic digestion has been widely investigated and applied as it promotes microbial retention time and enhances the efficiency. Previous studies on anaerobic biofilm primarily focused on application in wastewater treatment, while its role has been significantly extended to accelerate the degradation of lignocellulosic biomass, improve gas-liquid mass transfer for biogas upgrading, or enhance resistance to inhibitors or toxic pollutants. This work comprehensively reviewed the current applications of biofilm in anaerobic digestion and focused on impacting factors, optimization strategies, reactor set-up, and microbial communities. Moreover, a full-scale biofilm reactor case from Norway is also reported. This review provides a state of-the- art insight on the role of biofilm in anaerobic digestion.

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: Deciphering of performance, metabolic pathways and microbial communities

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.

Bioleaching of rare earth elements from ores and waste materials: Current status, economic viability and future prospects

Rare earth elements (REEs) are critical components of numerous products widely used in many areas, and the demand for REEs is increasing dramatically in recent years. Physical-chemical leaching is commonly adopted for the recovery of REEs from ores and solid wastes, but concerns over the generation of hazards, operation safety, and environmental pollution have urged the transition to greener and more sustainable leaching methods. Bioleaching is considered an excellent alternative for the recovery of REEs. This review provided an overview on the REEs recovery from primary and secondary resources via different bioleaching strategies. The techno-economics of bioleaching for REEs recovery were highlighted, and key factors affecting the economic viability of bioleaching were identified. Finally, strategies including the utilization of low-cost substrates as feedstocks, non-sterile bioleaching, recycling and reutilization of biolixiviants, and development of robust bioleaching strains were proposed to improve the economic competitiveness of bioleaching. It is expected that this review could serve as a useful guideline on the design of more economically competitive bioleaching processes for the recovery REEs from different resources.

Assembly of functional microbial ecosystems: from molecular circuits to communities

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.

Bacterial valorization of lignin for the sustainable production of value-added bioproducts

As the most abundant aromatic biopolymer in the biosphere, lignin represents a promising alternative feedstock for the industrial production of various value-added bioproducts with enhanced economical value. However, the large-scale implementation of lignin valorization remains challenging because of the heterogeneity and irregular structure of lignin. General fragmentation and depolymerization processes often yield various products, but these approaches necessitate tedious purification steps to isolate target products. Moreover, microbial biocatalytic processes, especially bacterial-based systems with high metabolic activity, can depolymerize and further utilize lignin in an eco-friendly way. Considering that wild bacterial strains have evolved several metabolic pathways and enzymatic systems for lignin degradation, substantial efforts have been made to exploit their potential for lignin valorization. This review summarizes recent advances in lignin valorization for the production of value-added bioproducts based on bacterial systems. Additionally, the remaining challenges and available strategies for lignin biodegradation processes and future trends of bacterial lignin valorization are discussed.

Microbial biofilms as a platform for diverse biocatalytic applications

Microbial biofilms have gained significant traction in commercial wastewater treatment due to their inherent resilience, well-organized structure, and potential for collaborative metabolic processes. As our understanding of their physiology deepens, these living catalysts are finding exciting applications beyond wastewater treatment, including the production of bulk and fine chemicals, bioelectricity generation, and enzyme immobilization. While the biological applications of biofilms in different biocatalytic systems have been extensively summarized, the applications of artificially engineered biofilms were rarely discussed. This review aims to bridge this gap by highlighting the untapped potential of engineered microbial biofilms in diverse biocatalytic applications, with a focus on strategies for biofilms engineering. Strategies for engineering biofilm-based systems will be explored, including genetic modification, synthetic biology approaches, and targeted manipulation of biofilm formation processes. Finally, the review will address key challenges and future directions in developing robust biofilm-based biocatalytic platforms for large-scale production of chemicals, pharmaceuticals, and biofuels.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

Polymer production is rapidly increasing, but there are no large-scale technologies available to effectively mitigate the massive accumulation of these recalcitrant materials. One potential solution is the development of a carbon-neutral polymer life cycle, where microorganisms convert plant biomass to chemicals, which are used to synthesize biodegradable materials that ultimately contribute to the growth of new plants. Realizing a circular carbon life cycle requires the integration of knowledge across microbiology, bioengineering, materials science, and organic chemistry, which itself has hindered large-scale industrial advances. This review addresses the biodegradation status of common synthetic polymers, identifying novel microbes and enzymes capable of metabolizing these recalcitrant materials and engineering approaches to enhance their biodegradation pathways. Design considerations for the next generation of biodegradable polymers are also reviewed, and finally, opportunities to apply findings from lignocellulosic biodegradation to the design and biodegradation of similarly recalcitrant synthetic polymers are discussed.

One-Pot Biocatalytic Route from Alkanes to α,ω-Diamines by Whole-Cell Consortia of Engineered Yarrowia lipolytica and Escherichia coli

Metabolically engineered microbial consortia can contribute as a promising production platform for the supply of polyamide monomers. To date, the biosynthesis of long-chain α,ω-diamines from n-alkanes is challenging because of the inert nature of n-alkanes and the complexity of the overall synthesis pathway. We combined an engineered Yarrowia lipolytica module with Escherichia coli modules to obtain a mixed strain microbial consortium that could catalyze an efficient biotransformation of n-alkanes into corresponding α,ω-diamines. The engineered Y. lipolytica strain was constructed (YALI10) wherein the two genes responsible for β-oxidation and the five genes responsible for the overoxidation of fatty aldehydes were deleted. This newly constructed YALI10 strain expressing transaminase (TA) could produce 0.2 mM 1,12-dodecanediamine (40.1 mg/L) from 10 mM n-dodecane. The microbial consortia comprising engineered Y. lipolytica strains for the oxidation of n-alkanes (OM) and an E. coli amination module (AM) expressing an aldehyde reductase (AHR) and transaminase (TA) improved the production of 1,12-diamine up to 1.95 mM (391 mg/L) from 10 mM n-dodecane. Finally, combining the E. coli reduction module (RM) expressing a carboxylic acid reductase (CAR) and an sfp phosphopantetheinyl transferase with OM and AM further improved the production of 1,12-diamine by catalyzing the reduction of undesired 1,12-diacids into 1,12-diols, which further undergo amination to give 1,12-diamine as the target product. This newly constructed mixed strain consortium comprising three modules in one pot gave 4.1 mM (41%; 816 mg/L) 1,12-diaminododecane from 10 mM n-dodecane. The whole-cell consortia reported herein present an elegant "greener" alternative for the biosynthesis of various α,ω-diamines (C8, C10, C12, and C14) from corresponding n-alkanes.

Synergistic effect of two bacterial strains promoting anaerobic digestion of rice straw to produce methane

A large amount of agricultural waste causes global environmental pollution. Biogas production by microbial pretreatment is an important way to utilize agricultural waste resources. In this study, Sporocytophaga CG-1 (A, cellulolytic strain) was co-cultured with Bacillus clausii HP-1 (B, non-cellulolytic strain) to analyze the effect of pretreatment of rice straw on methanogenic capacity of anaerobic digestion (AD). The results showed that weight loss rate of filter paper of co-culture combination is 53.38%, which is 29.37% higher than that of A. The synergistic effect of B on A can promote its degradation of cellulose. The cumulative methane production rate of the co-culture combination was the highest (93.04 mL/g VS substrate), which was significantly higher than that of A, B and the control group (82.38, 67.28 and 67.70 mL/g VS substrate). Auxiliary bacteria can improve cellulose degradation rate by promoting secondary product metabolism. These results provide data support for the application of co-culture strategies in the field of anaerobic digestion practices.

Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia

Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.

Research advances on the consolidated bioprocessing of lignocellulosic biomass

Lignocellulosic biomass is an abundant and renewable bioresource for the production of biofuels and biochemical products. The classical biorefinery process for lignocellulosic degradation and conversion comprises three stages, i.e., pretreatment, enzymatic saccharification, and fermentation. However, the complicated pretreatment process, high cost of cellulase production, and insufficient production performance of fermentation strains have restricted the industrialization of biorefinery. Consolidated bioprocessing (CBP) technology combines the process of enzyme production, enzymatic saccharification, and fermentation in a single bioreactor using a specific microorganism or a consortium of microbes and represents another approach worth exploring for the production of chemicals from lignocellulosic biomass. The present review summarizes the progress made in research of CBP technology for lignocellulosic biomass conversion. In this review, different CBP strategies in lignocellulose biorefinery are reviewed, including CBP with natural lignocellulose-degrading microorganisms as the chassis, CBP with biosynthetic microorganisms as the chassis, and CBP with microbial co-culturing systems. This review provides new perspectives and insights on the utilization of low-cost feedstock lignocellulosic biomass for production of biochemicals.

Maximizing the benefits of biofilms in fermentation processes

Biofilm-based fermentation has great potential, as it possesses inherent characteristics such as self-immobilization, high resistance to reactants, and long-term activity. This forum focuses on research targets for promoting biofilm engineering to maximize the beneficial features of biofilms and to effectively utilize them in biofilm-mediated fermentation.

Astragalus polysaccharide: implication for intestinal barrier, anti-inflammation, and animal production

Intestine is responsible for nutrients absorption and plays a key role in defending against various dietary allergens, antigens, toxins, and pathogens. Accumulating evidence reported a critical role of intestine in maintaining animal and human health. Since the use of antibiotics as growth promoters in animal feed has been restricted in many countries, alternatives to antibiotics have been globally investigated, and polysaccharides are considered as environmentally friendly and promising alternatives to improve intestinal health, which has become a research hotspot due to its antibiotic substitution effect. Astragalus polysaccharide (APS), a biological macromolecule, is extracted from astragalus and has been reported to exhibit complex biological activities involved in intestinal barrier integrity maintenance, intestinal microbiota regulation, short-chain fatty acids (SCFAs) production, and immune response regulation, which are critical for intestine health. The biological activity of APS is related to its chemical structure. In this review, we outlined the source and structure of APS, highlighted recent findings on the regulation of APS on physical barrier, biochemical barrier, immunological barrier, and immune response as well as the latest progress of APS as an antibiotic substitute in animal production. We hope this review could provide scientific basis and new insights for the application of APS in nutrition, clinical medicine and health by understanding particular effects of APS on intestine health, anti-inflammation, and animal production.

Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform

The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield. However, research on synthetic consortia is still in its infancy, with numerous challenges regarding the design and construction of stable synthetic consortia. This review provides a comprehensive comparison of the advantages and disadvantages of mono-culture systems and synthetic consortia. Key considerations for engineering synthetic consortia based on recent advances are summarized, and simulation and computational tools for guiding the advancement of synthetic consortia are discussed. Moreover, further development of more efficient and cost-effective synthetic consortia with emerging technologies such as artificial intelligence and machine learning is highlighted.

Structural and digestive characters of a heteropolysaccharide fraction from tea (Camellia sinensis L.) flower

Tea (Camellia sinensis L.) flower polysaccharides (TFPS) have various health-promoting functions. In the present work, the structure of a purified TFPS fraction, namely TFPS-1-3p, and its in vitro digestive properties were investigated. The results demonstrated that TFPS-1-3p was a typical heteropolysaccharide consisting of rhamnose (Rha), arabinose (Ara), galactose (Gal) and galacturonic acid (GalA) with a molecular weight of 47.77 kDa. The backbone of TFPS-1-3p contained → 4)-α-d-GalpA(-6-OMe)-(1 → 4)-α-GalpA-(1 → and → 4)-α-d-GalpA(-6-OMe)-(1 → 2,4)-α-l-Rhap-(1 → linkages. The branch linkages in TFPS-1-3p contained → 6)-β-d-Galp-(1→, →3,6)-β-d-Galp-(1→, →5)-α-l-Araf-(1 → and → 3,5)-α-l-Araf-(1 →. Subsequently, TFPS-1-3p could not be degraded under simulated human gastrointestinal conditions but could be of use to human fecal microbes, thereby lowering the pH and increasing the production of short-chain fatty acids (SCFAs) of the gut microenvironment and altering the composition of the gut microbiota. The relative abundance of Fusobacterium_mortiferum Megasphaera_elsdenii_DSM_20460, Bacteroides thetaiotaomicron, Bacteroides plebeius and Collinsella aerofaciens increased significantly, potentially contributing to the degradation of TFPS-1-3p.

Variation Among Japanese Miso Breweries in Indoor Microbiomes is Mainly Ascribed to Variation in Type of Indoor Surface

Miso is a microbially-fermented soybean food. The miso brewery indoor microbiome contributes to miso fermentation. Japanese breweries are not climate-controlled, so indoor spaces are strongly affected by the prevailing climate. Because climate influences microorganism distribution, our first hypothesis is that latitude, as a proxy for climate, is a major determinant of brewery indoor microbiome structure. Breweries vary in interior surface materials and in the way operations (steaming, processing, fermenting) are apportioned among rooms. Therefore, our second hypothesis is that more variability in indoor microbiomes exists among breweries than can be ascribed to a latitudinal gradient. Most miso produced today is inoculated with commercial microbial strains to standardize fermentation. If commercial strains outcompete indigenous microbes for membership in the indoor microbiome, this practice may homogenize indoor microbiomes among regions or breweries. Therefore, our third hypothesis is that inoculant fungal species dominate indoor fungal communities and make it impossible to distinguish communities among breweries or across their latitudinal gradient. We tested these hypotheses by sampling indoor surfaces in several breweries across a latitudinal gradient in Japan. We found that latitude had a significant but relatively small impact on indoor fungal and bacterial communities, that the effect of brewery was large relative to latitude, and that inoculant fungi made such small contributions to the indoor microbiome that distinctions among breweries and along the latitudinal gradient remained apparent. Recently, the Japanese Ministry of Agriculture, Forestry and Fisheries specified fungal inoculants to standardize miso production. However, this may not be possible so long as the indoor microbiome remains uncontrolled.

Energy and nutrient recovery from municipal and industrial waste and wastewater-a perspective

This publication highlights the latest advancements in the field of energy and nutrient recovery from organics rich municipal and industrial waste and wastewater. Energy and carbon rich waste streams are multifaceted, including municipal solid waste, industrial waste, agricultural by-products and residues, beached or residual seaweed biomass from post-harvest processing, and food waste, and are valuable resources to overcome current limitations with sustainable feedstock supply chains for biorefining approaches. The emphasis will be on the most recent scientific progress in the area, including the development of new and innovative technologies, such as microbial processes and the role of biofilms for the degradation of organic pollutants in wastewater, as well as the production of biofuels and value-added products from organic waste and wastewater streams. The carboxylate platform, which employs microbiomes to produce mixed carboxylic acids through methane-arrested anaerobic digestion, is the focus as a new conversion technology. Nutrient recycling from conventional waste streams such as wastewater and digestate, and the energetic valorization of such streams will also be discussed. The selected technologies significantly contribute to advanced waste and wastewater treatment and support the recovery and utilization of carboxylic acids as the basis to produce many useful and valuable products, including food and feed preservatives, human and animal health supplements, solvents, plasticizers, lubricants, and even biofuels such as sustainable aviation fuel.

ONE-SENTENCE SUMMARY

Multifaceted waste streams as the basis for resource recovery are essential to achieve environmental sustainability in a circular economy, and require the development of next-generation waste treatment technologies leveraging a highly adaptive mixed microbial community approach to produce new biochemicals, biomaterials, and biofuels from carbon-rich organic waste streams.

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted.

ONE-SENTENCE SUMMARY

This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

Re-considering and designing microbiomes for future waste biorefinery

It is an increasingly promising research direction using microbiomes to produce various chemicals in order to support people's growing need for sustainability. Currently, bottom-up constructed defined microbiomes and top-down constructed undefined microbiomes play an essential role in the fields of synthetic biology and environmental engineering, respectively. However, if we are goal-oriented and want to align scientific principles with technology and engineering in future waste biorefinery, we need to reconsider and design microbiomes interdisciplinarily. In this editorial, we briefly review the latest applications of two approaches to microbiome design (bottom-up and top-down) and the dilemmas faced in using complex waste. Consequently, we introduce the concept of 'sustainable synthetic microbiomics' to apply combined bottom-up and top-down constructed microbiomes to provide products for human needs from low-value waste. Furthermore, we outline the relatively comprehensive research contents and expected prospects based on the pressing problems. Finally, burning questions on key research contents are proposed for specific cases, hoping to provide valuable views for future microbiome biorefinery.

Customized spatial niches for synthetic microbial consortia

The construction of synthetic microbial consortia has been considered a new frontier. However, maintaining artificial microbial communities remains challenging because the dominant strain eventually outcompetes the others. Inspired by natural ecosystems, one promising approach to assemble stable consortia is to construct spatial niches partitioning subpopulations and overlapping abiotic requirements.

Metabolic division of labor between Acetivibrio thermocellus DSM 1313 and Thermoanaerobacterium thermosaccharolyticum MJ1 enhanced hydrogen production from lignocellulose

In this consortium, DSM 1313 was responsible for degrading lignocellulose by cellulosome, while the highly efficient hydrogen-producing bacterium MJ1 consumed the sugar produced by DSM 1313 to grow and produce more hydrogen. The results showed that the maximum hydrogen production of 259.57 mL/g substrate was obtained at the inoculation ratio (OD600) of 2:1 (DSM 1313:MJ1) and substrate concentration of 10 g/L, 70.84 % higher than pure culture. Furthermore, MJ1 dominated the co-culture system by using various sugars resulting from the biodegradation of substrate, thereby relieving the inhibition of sugar on DSM 1313 and leading to more hydrogen production. In the co-culture system, the value of extracellular oxidation-reduction potential and the ratio of NAD+/NADH was lower than that of pure culture. Additionally, at the gene level, [NiFe]-hydrogenase and [FeFe]-hydrogenase related enzymes were significantly up-regulated, leading to a two-fold increase in hydrogenase activity of co-culture compared with pure culture.

Enhancing scalability and economic viability of lignocellulose-derived biofuels production through integrated pretreatment and methanogenesis arrest

The pursuit of affordable biofuels necessitates continuous refinement of valorization strategies, focusing on cost-effective feedstocks, accessible bioprocessing, and high-quality products. High energy input required during various stages, including pretreatment, post-pretreatment, and methanogenesis arrest, impeded the economic lignocellulose-derived biofuels production from anaerobic digestion (AD). Addressing this challenge, an upstream process integrating synergistic alkali pretreatment and arrested AD was proposed. Results demonstrated that an optimum reactor pH 10 yielded a volatile fatty acids (VFA) titer of 3.6 gCOD/L, only 23% lower than using methanogenesis inhibitor. The study further explored the interplay between initial pH, cell viability/functionality, and VFA production by assessing cell viability and cell population demographics. This integrated approach demonstrated a VFA yield of 364 gVFA/kgTSsubstrate at a cost of just USD 0.2/kgVFA, encompassing post-pretreatment and methanogenesis arrest, which underscores the viability of combining pretreatment and methanogenesis arrest for cost effective and scalable biofuels production.

Construction of stable microbial consortia for effective biochemical synthesis

Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.

Global trends and future prospects of lactic acid production from lignocellulosic biomass

Lignocellulosic biomass (LCB) stands as a substantial and sustainable resource capable of addressing energy and environmental challenges. This study employs bibliometric analysis to investigate research trends in lactic acid (LA) production from LCB spanning the years 1991 to 2022. The analysis reveals a consistent growth trajectory with minor fluctuations in LA production from LCB. Notably, there's a significant upswing in publications since 2009. Bioresource Technology and Applied Microbiology and Biotechnology emerge as the top two journals with extensive contributions in the realm of LA production from LCB. China takes a prominent position in this research domain, boasting the highest total publication count (736), betweenness centrality value (0.30), and the number of collaborating countries (42), surpassing the USA and Japan by a considerable margin. The author keywords analysis provides valuable insights into the core themes in LA production from LCB. Furthermore, co-citation reference analysis delineates four principal domains related to LA production from LCB, with three associated with microbial conversion and one focused on chemical catalytic conversion. Additionally, this study examines commonly used LCB, microbial LA producers, and compares microbial fermentation to chemical catalytic conversion for LCB-based LA production, providing comprehensive insights into the current state of this field and suggesting future research directions.

Amoxicillin degradation and high-value extracellular polymer recovery by algal-bacterial symbiosis systems

Algal-bacterial symbiosis systems have emerged as sustainable methods for the treatment of new pollutants and the recovery of resources. However, the bio-refinery of biomass derived from microalgae is inefficient and expensive. In order to simultaneously degrade antibiotic and recover resources efficiently, two algal-bacterial symbiosis systems were constructed using Pseudomonas aeruginosa (alginate overproduction) and Bacillus subtilis (poly-γ-glutamic acid overproduction) with amoxicillin-degrading-microalga Prototheca zopfii W1. The optimal conditions for W1 to degrade amoxicillin are 35 °C, pH 7, and 180 rpm. In the presence of 5-50 mg/L of amoxicillin, W1-P. aeruginosa and W1-B. subtilis exhibit higher amoxicillin degradation and produce more extracellular polymers than W1 or bacteria alone. The metabolomic analysis demonstrates that the algal-bacterial symbiosis enhances the tolerance of W1 to amoxicillin by altering carbohydrate metabolism and promotes the production of biopolymers by upregulating the precursors synthesis. Moreover, the removal of amoxicillin (10 mg/L) from livestock effluent by W1-P. aeruginosa and W1-B. subtilis is greater than 90 % in 3 days, and the maximum yields of alginate and poly-γ-glutamate are 446.1 and 254.3 mg/g dry cell weight, respectively. These outcomes provide theoretical support for the application of algal-bacterial symbiosis systems to treatment of amoxicillin wastewater and efficient production of biopolymers.

Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice

Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.

Toward optimal use of biomass as carbon source for chemical bioproduction

Biomass is widely identified as a promising, renewable replacement for fossil feedstocks in the production of energy, fuels, and chemicals. However, the sustainable supply of biomass is limited. Economic and ecological criteria support prioritization of biomass as a carbon source for organic chemicals; however, utilization for energy currently dominates. Therefore, to optimize the use of available biomass feedstock, biorefining development must focus on high carbon efficiencies and enabling the conversion of all biomass fractions, including lignin and fermentation-derived CO₂. Additionally, novel technological platforms should allow the incorporation of nontraditional, currently underutilized carbon feedstocks (e.g. manure) into biorefining processes. To this end, funneling of waste feedstocks to a single product (e.g. methane) and subsequent conversion to chemicals is a promising approach.

Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study

Background

In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).

Results

The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.

Conclusions

We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.

Engineered Living Materials For Sustainability

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

Emerging enzyme surface display systems for waste resource recovery

The current century marks an inflection point for human progress, as the developed world increasingly comes to recognize that the ecological and socioeconomic impacts of resource extraction must be balanced with more sustainable modes of growth that are less reliant on non-renewable sources of energy and materials. This has opened a window of opportunity for cross-sector development of biotechnologies that harness the metabolic problem-solving power of microbial communities. In this context, recovery has emerged as an organizing principal to create value from industrial and municipal waste streams, and the search is on for new enzymes and platforms that can be used for waste resource recovery at scale. Enzyme surface display on cells or functionalized materials has emerged as a promising platform for waste valorization. Typically, surface display involves the use of substrate binding or catalytic domains of interest translationally fused with extracellular membrane proteins in a microbial chassis. Novel display systems with improved performance features include S-layer display with increased protein density, spore display with increased resistance to harsh conditions, and intracellular inclusions including DNA-free cells or nanoparticles with improved social licence for in situ applications. Combining these display systems with advances in bioprinting, electrospinning and high-throughput functional screening have potential to transform outmoded extractive paradigms into 'trans-metabolic" processes for remediation and waste resource recovery within an emerging circular bioeconomy.

Recent progress and challenges in biotechnological valorization of lignocellulosic materials: Towards sustainable biofuels and platform chemicals synthesis

Lignocellulosic materials (LCM) have garnered attention as feedstocks for second-generation biofuels and platform chemicals. With an estimated annual production of nearly 200 billion tons, LCM represent an abundant source of clean, renewable, and sustainable carbon that can be funneled to numerous biofuels and platform chemicals by sustainable microbial bioprocessing. However, the low bioavailability of LCM due to the recalcitrant nature of plant cell components, the complexity and compositional heterogeneity of LCM monomers, and the limited metabolic flexibility of wild-type product-forming microorganisms to simultaneously utilize various LCM monomers are major roadblocks. Several innovative strategies have been proposed recently to counter these issues and expedite the widespread commercialization of biorefineries using LCM as feedstocks. Herein, we critically summarize the recent advances in the biological valorization of LCM to value-added products. The review focuses on the progress achieved in the development of strategies that boost efficiency indicators such as yield and selectivity, minimize carbon losses via integrated biorefinery concepts, facilitate carbon co-metabolism and carbon-flux redirection towards targeted products using recently engineered microorganisms, and address specific product-related challenges, to provide perspectives on future research needs and developments. The strategies and views presented here could guide future studies in developing feasible and economically sustainable LCM-based biorefineries as a crucial node in achieving carbon neutrality.

Prospects for utilizing microbial consortia for lignin conversion

Naturally occurring microbial communities are able to decompose lignocellulosic biomass through the concerted production of a myriad of enzymes that degrade its polymeric components and assimilate the resulting breakdown compounds by members of the community. This process includes the conversion of lignin, the most recalcitrant component of lignocellulosic biomass and historically the most difficult to valorize in the context of a biorefinery. Although several fundamental questions on microbial conversion of lignin remain unanswered, it is known that some fungi and bacteria produce enzymes to break, internalize, and assimilate lignin-derived molecules. The interest in developing efficient biological lignin conversion approaches has led to a better understanding of the types of enzymes and organisms that can act on different types of lignin structures, the depolymerized compounds that can be released, and the products that can be generated through microbial biosynthetic pathways. It has become clear that the discovery and implementation of native or engineered microbial consortia could be a powerful tool to facilitate conversion and valorization of this underutilized polymer. Here we review recent approaches that employ isolated or synthetic microbial communities for lignin conversion to bioproducts, including the development of methods for tracking and predicting the behavior of these consortia, the most significant challenges that have been identified, and the possibilities that remain to be explored in this field.

Construction of microbial consortia for microbial degradation of complex compounds

Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use

Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.

Creative biological lignin conversion routes toward lignin valorization

Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.

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.

Agent-Based Modeling of Microbial Communities

Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.

Emerging Modification Technologies of Lignin-based Activated Carbon toward Advanced Applications

Lignin-based activated carbon (LAC) is a promising high-quality functional material due to high surface area, abundant porous structure, and various functional groups. Modification is the most important step to functionalize LAC by altering its porous and chemical properties. This Review summarizes the state-of-the-art modification technologies of LAC toward advanced applications. Promising modification approaches are reviewed to display their effects on the preparation of LAC. The multiscale changes in the porosity and the surface chemistry of LAC are fully discussed. Advanced applications are then introduced to show the potential of LAC for supercapacitor electrode, catalyst support, hydrogen storage, and carbon dioxide capture. Finally, the mechanistic structure-function relationships of LAC are elaborated. These results highlight that modification technologies play a special role in altering the properties and defining the functionalities of LAC, which could be a promising porous carbon material toward industrial applications.

Toward predictive engineering of gene circuits

Many synthetic biology applications rely on programming living cells using gene circuits - the assembly and wiring of genetic elements to control cellular behaviors. Extensive progress has been made in constructing gene circuits with diverse functions and applications. For many circuit functions, however, it remains challenging to ensure that the circuits operate in a predictable manner. Although the notion of predictability may appear intuitive, close inspection suggests that it is not always clear what constitutes predictability. We dissect this concept and how it can be confounded by the complexity of a circuit, the complexity of the context, and the interplay between the two. We discuss circuit engineering strategies, in both computation and experiment, that have been used to improve the predictability of gene circuits.