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.

Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.

Novel processing strategies to enhance the bioaccessibility and bioavailability of functional components in wheat bran

Dietary fiber, polysaccharides and phenols are the representative functional components in wheat bran, which have important nutritional properties and pharmacological effects. However, the most functional components in wheat bran exist in bound form with low bioaccessibility. This paper reviews these functional components, analyzes modification methods, and focuses on novel solid-state fermentation (SSF) strategies in the release of functional components. Mining efficient microbial resources from traditional fermented foods, exploring the law of material exchange between cell populations, and building a stable self-regulation co-culture system are expected to strengthen the SSF process. In addition, emerging biotechnology such as synthetic biology and genome editing are used to transform the mixed fermentation system. Furthermore, combined with the emerging physical-field pretreatment coupled with SSF strategies applied to the modification of wheat bran, which provides a theoretical basis for the high-value utilization of wheat bran and the development of related functional foods and drugs.

Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks

The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.

Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system

Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.

Improving production of lactic acid and volatile fatty acids from dairy cattle manure and corn straw silage: Effects of mixing ratios and temperature

Anaerobic co-fermentation (AcoF) of dairy cattle manure (DCM) and corn straw silage (CSS) for producing lactic acid (LA) and volatile fatty acids (VFAs) was investigated. Batch experiments were conducted at seven different DCM/CSS ratios and at mesophilic and thermophilic temperatures. Results indicated that the highest concentration of LA was 17.50 ± 0.70 g/L at DCM:CSS ratio of 1:3 and thermophilic temperature, while VFAs was 18.23 ± 2.45 g/L at mono-CSS fermentation and mesophilic temperature. High solubilization of thermophilic conditions contributed to LA accumulation in AcoF process. Presence of the CSS increased the relative abundance of Lactobacillus for LA production at thermophilic. Meanwhile, the abundance of Bifidobacterium was increased when CSS was added at mesophilic, which could conduce to VFAs production. This study provides a new route for enhancing the biotransformation of DCM and CSS into short-chain fatty acids, potentially bringing economic benefits to agricultural waste treatment.

Unveiling the mechanism for selective cleavage of C-C bonds in sugar reactions on tungsten trioxide-based catalysts

Conversion of naturally occurring sugars, the most abundant biomass resources on Earth, to fuels and chemicals provides a sustainable and carbon-neutral alternative to the current fossil resource-based processes. Tungsten-based catalysts (e.g., WO3) are efficient for selectively cleaving C-C bonds of sugars to C2,3 oxygenate intermediates (e.g., glycolaldehyde) that can serve as platform molecules with high viability and versatility in the synthesis of various chemicals. Such C-C bond cleavage follows a mechanism distinct from the classical retro-aldol condensation. Kinetic, isotope 13C-labeling, and spectroscopic studies and theoretical calculations, reveal that the reaction proceeds via a surface tridentate complex as the critical intermediate on WO3, formed by chelating both α- and β-hydroxyls of sugars, together with the carbonyl group, with two adjacent tungsten atoms (W-O-W) contributing to the β-C-C bond cleavage. This mechanism provides insights into sugar chemistry and enables the rational design of catalytic sites and reaction pathways toward the efficient utilization of sugar-based feedstocks.

Current Advances in Biodegradation of Polyolefins

Polyolefins, including polyethylene (PE), polypropylene (PP) and polystyrene (PS), are widely used plastics in our daily life. The excessive use of plastics and improper handling methods cause considerable pollution in the environment, as well as waste of energy. The biodegradation of polyolefins seems to be an environmentally friendly and low-energy consumption method for plastics degradation. Many strains that could degrade polyolefins have been isolated from the environment. Some enzymes have also been identified with the function of polyolefin degradation. With the development of synthetic biology and metabolic engineering strategies, engineered strains could be used to degrade plastics. This review summarizes the current advances in polyolefin degradation, including isolated and engineered strains, enzymes and related pathways. Furthermore, a novel strategy for polyolefin degradation by artificial microbial consortia is proposed, which would be helpful for the efficient degradation of polyolefin.

Toward merging bottom-up and top-down model-based designing of synthetic microbial communities

The increasing interest of microbial communities as promising biocatalyst is leading an intense effort into the development of computational frameworks assisting the analysis and rational engineering of such complex ecosystems. Here, we critically review the recent computational and model-guided advances in the system-level engineering of microbiome, including both the rational bottom-up and the evolutionary top-down approaches. Furthermore, we highlight modeling and computational methods supporting both engineering paradigms. Finally, we discuss the advantages of combining both strategies into a hybrid top-down/bottom-up (middle-out) strategy to engineer synthetic microbial communities with improved performance and scope.

Progress of engineered bacteria for tumor therapy

Recently, with the rapid development of bioengineering technology and nanotechnology, natural bacteria were modified to change their physiological activities and therapeutic functions for improved therapeutic efficiency of diseases. These engineered bacteria were equipped to achieve directed genetic reprogramming, selective functional reorganization and precise spatio-temporal control. In this review, research progress in the basic modification methodologies of engineered bacteria were summarized, and representative researches about their therapeutic performances for tumor treatment were illustrated. Moreover, the strategies for the construction of engineered colonies based on engineering of individual bacteria were summarized, providing innovative ideas for complex functions and efficient anti-tumor treatment. Finally, current limitation and challenges of tumor therapy utilizing engineered bacteria were discussed.

Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei

Background

A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown.

Results

We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose.

Conclusions

Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01809-1.

Applications of synthetic light-driven microbial consortia for biochemicals production

Synthetic microbial consortia provide a versatile and efficient platform for biochemicals production through the labor division. Especially, microbial communities composed of phototrophs and heterotrophs offer a promising alternative, as they can directly convert carbon dioxide (CO₂) into chemicals. Within this system, photoautotrophic microbes can convert CO₂ into organic carbon for microbial growth and metabolites synthesis by the heterotrophic partners. In return, heterotrophs can provide additional CO₂ to support the growth of photoautotrophic microbes. However, the unmatched growing conditions, low stability and production efficiency of synthetic microbial consortia hinder their further applications. Thus, design and construction of mutualistic and stable synthetic light-driven microbial consortia are urgently needed. In this review, the progress of synthetic light-driven microbial consortia for chemicals production was comprehensively summarized. In addition, space-efficient synthetic light-driven microbial consortia in hydrogel system were reviewed. Perspectives on orderly distribution of light-driven microbial consortia associated with 3D printing technology in biomanufacturing were also addressed.

Bioconversion of food and lignocellulosic wastes employing sugar platform: A review of enzymatic hydrolysis and kinetics

Bioenergy and biochemicals can be sustainably produced through fermentation and anaerobic digestion (AD). However, this bioconversion processes could be more economical if the hydrolysis rates of substrates in bioreactors can be accelerated. In this review, the feasibilities of including enzymatic hydrolysis (EH) in various bioconversion systems were studied to facilitate the biological synergy. The reaction kinetics of EH in bioconversion systems comparing pretreated lignocellulosic biomass (LCB) and food waste (FW) substrates were reviewed. Possible strategies to improve the hydrolysis efficiency were explored, including co-cultivation during enzyme production and replacement of pure enzyme with on-site produced fungal mash during EH. Key insights into improvement of current AD and fermentation technologies were summarized and further formed into suggestions of future directions in techno-economic feasibility of biorefinery using mixture of the first-generation food crop feedstock with FW; and/or co-digestion of FW with LCB.

Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture

BACKGROUND

The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enriched communities.

RESULTS

By progressively shortening the hydraulic retention time (HRT) from 8 to 2 days with different temporal schemes in two bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing machine learning algorithms using 16S rRNA genes to predict n-caproate and n-caprylate productivities. Our dataset consisted of 14 and 40 samples from HRT of 8 and 2 days, respectively. Because of the size and balance of our dataset, we compared linear regression, support vector machine and random forest regression algorithms using the original and balanced datasets generated using synthetic minority oversampling. Further, we performed cross-validation to estimate model stability. The random forest regression was the best algorithm producing more consistent results with median of error rates below 8%. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter HRT. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.

CONCLUSIONS

Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterizing and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and microbial systems where community dynamics is linked to key functions. The general methodology used here can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites. Video Abstract.

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

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

Polymer Encapsulation of Bacterial Biosensors Enables Coculture with Mammalian Cells

Coexistence of different populations of cells and isolation of tasks can provide enhanced robustness and adaptability or impart new functionalities to a culture. However, generating stable cocultures involving cells with vastly different growth rates can be challenging. To address this, we developed living analytics in a multilayer polymer shell (LAMPS), an encapsulation method that facilitates the coculture of mammalian and bacterial cells. We leverage LAMPS to preprogram a separation of tasks within the coculture: growth and therapeutic protein production by the mammalian cells and l-lactate biosensing by Escherichia coli encapsulated within LAMPS. LAMPS enable the formation of a synthetic bacterial-mammalian cell interaction that enables a living biosensor to be integrated into a biomanufacturing process. Our work serves as a proof-of-concept for further applications in bioprocessing since LAMPS combine the simplicity and flexibility of a bacterial biosensor with a viable method to prevent runaway growth that would disturb mammalian cell physiology.

Chitosan-modified fluorescent dye for simple, fast, and in-situ measurement of fungal cell growth in the presence of insoluble compounds

The measurement of fungal cell growth in submerged culture systems containing insoluble compounds is essential yet difficult due to the interferences from the insoluble compounds like biopolymers. Here, we developed a fluorescent strategy based on chitosan-modified fluorescein isothiocyanate (GC-FITC) to monitor the cell growth of lignocellulosic fungi cultivated on biopolymers. GC-FITC could stain only lignocellulosic fungi (Tricoderma reesei, Penicillium oxalicum, Aspergillus nidulans, and Neurospora crassa), but not biopolymers (cellulose, xylan, pectin, or lignin), excluding the interferences from these insoluble biopolymer. Moreover, a linear relationship was observed between the fluorescence intensity of GC-FITC absorbed by lignocellulosic fungi and the biomass of lignocellulosic fungi. Therefore, GC-FITC was leveraged to monitor the cell growth of lignocellulosic fungi when using biopolymers like cellulose as the carbon sources, which is faster, more convenient, time-saving, and cost-effective than the existing methods using protein/DNA content measurement. GC-FITC offers a powerful tool to detect fungal growth in culture systems with insoluble materials.

Future landscape of renewable fuel resources: Current and future conservation and utilization of main biofuel crops in China

Biofuel crops are one of the most promising regenerative alternatives of energy resources to fossil fuels. Revealing the current and future resource distribution patterns of biofuel crops will promote the development of green energies and the mitigation of greenhouse gas emissions. In this study, we first conducted a comprehensive and systematic analysis on the distribution patterns of main biofuel crops in China, using 22,352 occurrence records of 31 biofuel plant species and thirty-year environmental variables (1970-2000) with maximum entropy modeling, as well as nine-year field investigation of land use (2011-2019). The results showed that there were six different sub-regions for main biofuel crops in China, while Southwest China and South China were determined as the main concentrated potential regions. Specifically, the ranges of these regions were wider than those of current land use of main biofuel crops in China, indicating great potential for industrial cultivation. Moreover, the main biofuel crops had diverse changing patterns including increase, decrease and unstable under future climate change. Among them, biofuel crops with increase pattern (six crops) and decrease pattern (seven crops) should receive high attention for future resource utilization and production. Further field validation results confirmed that the above distribution patterns were mainly determined by increasing global temperature and precipitation. Collectively, these results will provide valuable references for the utilization and development of main biofuel resources under climate change in China, thereby shedding light on studies regarding the production of green biofuels globally.

Microhabitat drive microbial anabolism to promote carbon sequestration during composting

Transforming organic waste into stable carbon by composting is an eco-friendly way. However, the complex environment, huge microbial community and complicated metabolic of composting have limited the directional transformation of organic carbon, which is also not conducive to the fixation of organic carbon. Therefore, this review is based on the formation of humus, a stable by-product of composting, to expound how to promote carbon fixation by increasing the yield of humus. Firstly, we have clarified the transformation regularity of organic matter during composting. Meanwhile, the microhabitat factors affecting microbial catabolism and anabolism were deeply analyzed, in order to provide a theoretical basis for the micro habitat regulation of directional transformation of organic matter during composting. Given that, a method to adjust the directional humification and stabilization of organic carbon has been proposed. Hoping the rapid reduction and efficient stabilization of organic waste can be realized according to this method.

3D Printed Biocatalytic Living Materials with Dual-Network Reinforced Bioinks

The field of living materials seeks to harness living cells as microfactories that can construct a material itself or enhance the performance of material in some manner. While recent advances in 3D printing allow microbe manipulation to create bespoke living materials, the effective coupling of these living components in reinforced bioink designs remains a major challenge due to the difficulty in building a robust and cell-friendly microenvironment. Here, a type of dual-network bioink is reported for the 3D printing of living materials with enhanced biocatalysis capabilities, where bioinks are readily printable and provide a biocompatible environment along with desirable mechanical performance. It is demonstrated that integrating microbes into these bioinks enables the direct printing of catalytically living materials with high cell viability and maintains metabolic activity, which those living materials can be preserved and reused. Further, a bacteria-algae coculture system is fabricated for the bioremediation of chemicals, giving rise to its potential field applications.

Thermophiles: potential chassis for lignocellulosic biorefinery

Lignocellulosic thermophiles can speed up lignocellulose hydrolysis and promote efficient degradation, but limited genetic tools and heavy metabolic burden narrow the spectrum of potential products. Constructing synthetic microbial consortia is a potential strategy to address this bottleneck and improves the efficiency of lignocellulosic biorefineries.

Biofabrication and characterization of multispecies electroactive biofilms in stratified paper-based scaffolds

This work develops novel biofabrication and analysis platforms by creating innovative, paper-based 3-D systems that accurately recapitulate the structure, function, and physiology of living multispecies biofilms.

Biohydrogen production by mixed culture of Megasphaera elsdenii with lactic acid bacteria as Lactate-driven dark fermentation

Numerous attempts have been made to upscale biohydrogen production via dark fermentation (DF); however, the Achilles' heel of DF, i.e., lactic acid bacteria (LAB) contamination and overgrowth, hinders such upscaling. Key microbes are needed to develop a lactate-driven DF system that can serve as a lactate fermentation platform. In this study, the utility of Megasphaera elsdenii and LAB co-culturing in lactate-driven DF was evaluated. When inoculated simultaneously with LAB or after LAB culture, M. elsdenii achieved a stable hydrogen yield of 0.95-1.49 H₂-mol/mol-glucose, approximately half that obtained in pure M. elsdenii cultures. Hydrogen production was maintained even at an initial M. elsdenii-to-LAB cell ratio of one-millionth or less. Moreover, M. elsdenii produced hydrogen via lactate-driven DF from unusable sugars such as xylose or cellobiose. Thus, M. elsdenii could be a Game changer instrumental in unlocking the full potential of DF.

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.

Function-driven design of Bacillus kochii and Filobasidium magnum co-culture to improve quality of flue-cured tobacco

Flue-cured tobacco (FCT) is an economical raw material whose quality affects the quality and cost of the derived product. However, the time-consuming and inefficient spontaneous aging is the primary process for improving the FCT quality in the industry. In this study, a function-driven co-culture with functional microorganisms was built in response to the quality-driven need for less irritation and more aroma in FCT. The previous study has found that Bacillus kochii SC could degrade starch and protein to reduce tobacco irritation and off-flavors. The Filobasidium magnum F7 with high lipoxygenase activity was screened out for degrading higher fatty acid esters and terpenoids to promote the aroma and flavor of FCT. Co-cultivation with strain SC and F7 obtained better quality improvement than mono-culture at an initial inoculation ratio of 1:3 for 2 days, representing a significant breakthrough in efficiency and a reduction in production costs compared to the more than 2 years required for the spontaneous aging process. Through the analysis of microbial diversity, predicted flora functions, enzyme activities and volatile compositions within the mono- and co-cultivation, our study showed the formation of a function-driven co-culture between two strains through functional division of labor and nutritional feeding. Herein, the function-driven co-culture via bioaugmentation will become an increasingly implemented approach for the tobacco industry.

Source separation, transportation, pretreatment, and valorization of municipal solid waste: a critical review

Waste sorting is an effective means of enhancing resource or energy recovery from municipal solid waste (MSW). Waste sorting management system is not limited to source separation, but also involves at least three stages, i.e., collection and transportation (C&T), pretreatment, and resource utilization. This review focuses on the whole process of MSW management strategy based on the waste sorting perspective. Firstly, as the sources of MSW play an essential role in the means of subsequent valorization, the factors affecting the generation of MSW and its prediction methods are introduced. Secondly, a detailed comparison of approaches to source separation across countries is presented. Constructing a top-down management system and incentivizing or constraining residents' sorting behavior from the bottom up is believed to be a practical approach to promote source separation. Then, the current state of C&T techniques and its network optimization are reviewed, facilitated by artificial intelligence (AI) and the Internet of Things technologies. Furthermore, the advances in pretreatment strategies for enhanced sorting and resource recovery are introduced briefly. Finally, appropriate methods to valorize different MSW are proposed. It is worth noting that new technologies, such as AI, show high application potential in waste management. The sharing of (intermediate) products or energy of varying processing units will inject vitality into the waste management network and achieve sustainable development.

Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate

Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals.

Evaluation of PET Degradation Using Artificial Microbial Consortia

Polyethylene terephthalate (PET) biodegradation is regarded as an environmentally friendly degradation method. In this study, an artificial microbial consortium composed of Rhodococcus jostii, Pseudomonas putida and two metabolically engineered Bacillus subtilis was constructed to degrade PET. First, a two-species microbial consortium was constructed with two engineered B. subtilis that could secrete PET hydrolase (PETase) and monohydroxyethyl terephthalate hydrolase (MHETase), respectively; it could degrade 13.6% (weight loss) of the PET film within 7 days. A three-species microbial consortium was further obtained by adding R. jostii to reduce the inhibition caused by terephthalic acid (TPA), a breakdown product of PET. The weight of PET film was reduced by 31.2% within 3 days, achieving about 17.6% improvement compared with the two-species microbial consortium. Finally, P. putida was introduced to reduce the inhibition caused by ethylene glycol (EG), another breakdown product of PET, obtaining a four-species microbial consortium. With the four-species consortium, the weight loss of PET film reached 23.2% under ambient temperature. This study constructed and evaluated the artificial microbial consortia in PET degradation, which demonstrated the great potential of artificial microbial consortia in the utilization of complex substrates, providing new insights for biodegradation of complex polymers.

Exploring the optimization of aerobic food waste digestion efficiency through the engineering of functional biofilm Bio-carriers

The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion.

Reprogramming microbial populations using a programmed lysis system to improve chemical production

Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.

Engineered microbial consortia: strategies and applications

Many applications of microbial synthetic biology, such as metabolic engineering and biocomputing, are increasing in design complexity. Implementing complex tasks in single populations can be a challenge because large genetic circuits can be burdensome and difficult to optimize. To overcome these limitations, microbial consortia can be engineered to distribute complex tasks among multiple populations. Recent studies have made substantial progress in programming microbial consortia for both basic understanding and potential applications. Microbial consortia have been designed through diverse strategies, including programming mutualistic interactions, using programmed population control to prevent overgrowth of individual populations, and spatial segregation to reduce competition. Here, we highlight the role of microbial consortia in the advances of metabolic engineering, biofilm production for engineered living materials, biocomputing, and biosensing. Additionally, we discuss the challenges for future research in microbial consortia.

Customized materials-assisted microorganisms in tumor therapeutics

Microorganisms have been extensively applied as active biotherapeutic agents or drug delivery vehicles for antitumor treatment because of their unparalleled bio-functionalities. Taking advantage of the living attributes of microorganisms, a new avenue has been opened in anticancer research. The integration of customized functional materials with living microorganisms has demonstrated unprecedented potential in solving existing questions and even conferring microorganisms with updated antitumor abilities and has also provided an innovative train of thought for enhancing the efficacy of microorganism-based tumor therapy. In this review, we have summarized the emerging development of customized materials-assisted microorganisms (MAMO) (including bacteria, viruses, fungi, microalgae, as well as their components) in tumor therapeutics with an emphasis on the rational utilization of chosen microorganisms and tailored materials, the ingenious design of biohybrid systems, and the efficacious antitumor mechanisms. The future perspectives and challenges in this field are also discussed.

Processive Enzymes Kept on a Leash: How Cellulase Activity in Multienzyme Complexes Directs Nanoscale Deconstruction of Cellulose

Biological deconstruction of polymer materials gains efficiency from the spatiotemporally coordinated action of enzymes with synergetic function in polymer chain depolymerization. To perpetuate enzyme synergy on a solid substrate undergoing deconstruction, the overall attack must alternate between focusing the individual enzymes locally and dissipating them again to other surface sites. Natural cellulases working as multienzyme complexes assembled on a scaffold protein (the cellulosome) maximize the effect of local concentration yet restrain the dispersion of individual enzymes. Here, with evidence from real-time atomic force microscopy to track nanoscale deconstruction of single cellulose fibers, we show that the cellulosome forces the fiber degradation into the transversal direction, to produce smaller fragments from multiple local attacks ("cuts"). Noncomplexed enzymes, as in fungal cellulases or obtained by dissociating the cellulosome, release the confining force so that fiber degradation proceeds laterally, observed as directed ablation of surface fibrils and leading to whole fiber "thinning". Processive cellulases that are enabled to freely disperse evoke the lateral degradation and determine its efficiency. Our results suggest that among natural cellulases, the dispersed enzymes are more generally and globally effective in depolymerization, while the cellulosome represents a specialized, fiber-fragmenting machinery.

Rugose small colony variant and its hyper-biofilm in Pseudomonas aeruginosa: Adaption, evolution, and biotechnological potential

One of the hallmarks of the environmental bacterium Pseudomonas aeruginosa is its excellent ecological flexibility, which can thrive in diverse ecological niches. In different ecosystems, P. aeruginosa may use different strategies to survive, such as forming biofilms in crude oil environment, converting to mucoid phenotype in the cystic fibrosis (CF) lung, or becoming persisters when treated with antibiotics. Rugose small colony variants (RSCVs) are the adaptive mutants of P. aeruginosa, which can be frequently isolated from chronic infections. During the past years, there has been a renewed interest in using P. aeruginosa as a model organism to investigate the RSCVs formation, persistence and pathogenesis, as RSCVs represent a hyper-biofilm formation, high adaptability, high-tolerance sub-population in biofilms. This review will briefly summarize recent advances regarding the phenotypic, genetic and host interaction associated with RSCVs, with an emphasis on P. aeruginosa. Meanwhile, some non-pathogenic bacteria such as Pseudomonas fluorescence, Pseudomonas putida and Bacillus subtilis will be also included. Remarkable emphasis is given on intrinsic functions of such hyper-biofilm formation characteristic as well as its potential applications in several biocatalytic transformations including wastewater treatment, microbial fermentation, and plastic degradation. Hopefully, this review will attract the interest of researchers in various fields and shape future research focused not only on evolutionary biology but also on biotechnological applications related to RSCVs.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion

Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.

Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia

In this study, we examined a synthetic microbial consortium, composed of two selected bacteria, i.e., Citrobacter freundii so4 and Sphingobacterium multivorum w15, next to the fungus Coniochaeta sp. 2T2.1, with respect to their fate and roles in the degradation of wheat straw (WS). A special focus was placed on the effects of pH (7.2, 6.2, or 5.2), temperature (25 versus 28 °C), and shaking speed (60 versus 180 rpm). Coniochaeta sp. 2T2.1 consistently had a key role in the degradation process, with the two bacteria having additional roles. Whereas temperature exerted only minor effects on the degradation, pH and shaking speed were key determinants of both organismal growth and WS degradation levels. In detail, the three-partner degrader consortium showed significantly higher WS degradation values at pH 6.2 and 5.2 than at pH 7.2. Moreover, the two bacteria revealed up to tenfold enhanced final cell densities (ranging from log8.0 to log9.0 colony forming unit (CFU)/mL) in the presence of Coniochaeta sp. 2T2.1 than when growing alone or in a bacterial bi-culture, regardless of pH range or shaking speed. Conversely, at 180 rpm, fungal growth was clearly suppressed by the presence of the bacteria at pH 5.2 and pH 6.2, but not at pH 7.2. In contrast, at 60 rpm, the presence of the bacteria fostered fungal growth. In these latter cultures, oxygen levels were significantly lowered as compared to the maximal levels found at 180 rpm (about 5.67 mg/L, ~ 62% of saturation). Conspicuous effects on biomass appearance pointed to a fungal biofilm–modulating role of the bacteria.

Key points

• Coniochaeta sp. 2T2.1 has a key role in wheat straw (WS) degradation.

• Bacterial impact shifts when conditions change.

• pH and shaking speed are key drivers of the growth dynamics and WS degradation.

Harnessing lactic acid bacteria in synthetic microbial consortia

Lactic acid bacteria (LAB) are important members in synthetic microbial consortia due to their 'generally recognized as safe' status and diverse metabolic activities. Defined communities with LAB show great potential in elucidating metabolic interactions that drive their assembly and demonstrating power to address sustainability challenges in food, environment, and health.

A Lignocellulolytic Colletotrichum sp. OH with Broad-Spectrum Tolerance to Lignocellulosic Pretreatment Compounds and Derivatives and the Efficiency to Produce Hydrogen Peroxide and 5-Hydroxymethylfurfural Tolerant Cellulases

Fungal endophytes are an emerging source of novel traits and biomolecules suitable for lignocellulosic biomass treatment. This work documents the toxicity tolerance of Colletotrichum sp. OH toward various lignocellulosic pretreatment-derived inhibitors. The effects of aldehydes (vanillin, p-hydroxybenzaldehyde, furfural, 5-hydroxymethylfurfural; HMF), acids (gallic, formic, levulinic, and p-hydroxybenzoic acid), phenolics (hydroquinone, p-coumaric acid), and two pretreatment chemicals (hydrogen peroxide and ionic liquid), on the mycelium growth, biomass accumulation, and lignocellulolytic enzyme activities, were tested. The reported Colletotrichum sp. OH was naturally tolerant to high concentrations of single inhibitors like HMF (IC50; 17.5 mM), levulinic acid (IC50; 29.7 mM), hydroquinone (IC50; 10.76 mM), and H2O2 (IC50; 50 mM). The lignocellulolytic enzymes displayed a wide range of single and mixed inhibitor tolerance profiles. The enzymes β-glucosidase and endoglucanase showed H2O2- and HMF-dependent activity enhancements. The enzyme β-glucosidase activity was 34% higher in 75 mM and retained 20% activity in 125 mM H2O2. Further, β-glucosidase activity increased to 24 and 32% in the presence of 17.76 and 8.8 mM HMF. This research suggests that the Colletotrichum sp. OH, or its enzymes, can be used to pretreat plant biomass, hydrolyze it, and remove inhibitory by-products.

Challenges and Future Perspectives of Promising Biotechnologies for Lignocellulosic Biorefinery

Lignocellulose is a kind of renewable bioresource containing abundant polysaccharides, which can be used for biochemicals and biofuels production. However, the complex structure hinders the final efficiency of lignocellulosic biorefinery. This review comprehensively summarizes the hydrolases and typical microorganisms for lignocellulosic degradation. Moreover, the commonly used bioprocesses for lignocellulosic biorefinery are also discussed, including separated hydrolysis and fermentation, simultaneous saccharification and fermentation and consolidated bioprocessing. Among these methods, construction of microbial co-culturing systems via consolidated bioprocessing is regarded as a potential strategy to efficiently produce biochemicals and biofuels, providing theoretical direction for constructing efficient and stable biorefinery process system in the future.

Reprogramming Escherichia coli Metabolism for Bioplastics Synthesis from Waste Cooking Oil

The recycle and reutilization of food wastes is a promising alternative for supporting and facilitating circular economy. However, engineering industrially relevant model organisms to use food wastes as their sole carbon source has remained an outstanding challenge so far. Here, we reprogrammed Escherichia coli metabolism using modular pathway engineering followed by laboratory adaptive evolution to establish a strain that can efficiently utilize waste cooking oil (WCO) as the sole carbon source to produce monomers of bioplastics, namely, medium-chain α,ω-dicarboxylic acids (MCDCAs). First, the biosynthetic pathway of MCDCAs was designed and rewired by modifying the β-oxidation pathway and introducing an ω-oxidation pathway. Then, metabolic engineering and laboratory adaptive evolution were applied for improving the pathway efficiency of fatty acids utilization. Finally, the engineered strain E. coli AA0306 was able to produce 15.26 g/L MCDCAs with WCO as the sole carbon source. This study provides an economically attractive strategy for biomanufacturing bioplastics from food wastes, which has a great potentiality to be developed as a wide range of enabling biotechnologies for achieving green revolution.

Techno-economic assessment of bioethanol production from lignocellulose by consortium-based consolidated bioprocessing at industrial scale

Lignocellulose-based biofuels are of major importance to mitigate the impact of international traffic and transport on climate change while sustaining agricultural land for food supply. Highly integrated systems like consolidated bioprocessing (CBP), where enzyme production, enzymatic hydrolysis and fermentation of the released sugars are carried out in one reactor, offer the highest potential to save costs and to make lignocellulose-based biofuels economically competitive. The work described here showed that CBP based on a microbial consortium operated at full-scale (2,000 t/d) saves up to 27.5% of the total ethanol production costs compared to conventional ethanol production from lignocellulose in individual process steps. The cost savings are mainly achieved through lower CAPEX due to less apparatus requirements because of the integrated process, as well as through lower OPEX since no glucose is needed for enzyme production. A comparison with literature estimations of cost savings of CBP based on genetically modified microorganisms results in approximately the same range. As a result of a detailed sensitivity analysis, scale and yield were identified as the main cost-pushers from a process point of view, whereas the price level of the plant location has the highest impact on the investment conditions. In the EU, CBP yields enough margin for profitable production and the possibility to decentralize biomass valorization, whereas in the world's largest ethanol market, the U.S, profitable production of lignocellulosic ethanol can only be achieved by CBP combined with other cost saving techniques, such as utilization of cost-free waste feedstocks, since ethanol has undergone a considerable price slump.

Future directions of material chemistry and energy chemistry

Energy is an important substantial foundation for the survival and development of humans. However, the over-consumption of resources and environmental pollution have become more prominent. The key factors for solving energy problems are to increase energy utilization efficiency and optimize energy structure. The development of new materials is the research emphasis in the field of material chemistry all the time. For instance, developing new light-capture materials and catalysts to improve the efficiency of existing photovoltaic cells is one of the most effective approaches to increasing solar power capacity radically. The design of high-performance catalytic materials to make better use of energy from fossil fuels and biomass. In addition, it is an important research direction of material chemistry and energy chemistry to deeply understand the reaction mechanism of energy conversion.