Biotechnology for Biofuels

Given the current global environmental challenges, waste biomass is an attractive renewable resource for circular economies. Gasification of biomass yields syngas (CO, CO2, and H2) that is a suitable feedstock for gas fermentation in biomanufacturing of fuels and chemicals using acetogen microbes. While it is generally known that syngas composition influences both acetogen growth and process performance, we are lacking a consistent dataset quantifying these effects under controlled fermentation conditions. Here, we mapped the metabolic response of the model-acetogen Clostridium autoethanogenum to seven synthetic syngas mixtures during exponential batch growth in bioreactor fermentations. Notably, distinct gas compositions resulted in different fermentation profiles, affecting both growth and metabolite production. Maximum specific growth rates ranged within 0.05 0.13 h-1, with slower growth for low-CO mixtures. While acetate and ethanol production yields varied between 20-133 and 76-353 mmol per gram dry cell weight, respectively, minor production of 2,3-butanediol was detected. All syngas mixtures supported co-utilization of CO and H2, though gas uptake stoichiometry only moderately correlated with syngas content. Importantly, gas uptake stoichiometry strongly influenced carbon partitioning, with higher relative H2 uptake reducing CO2 loss or even realizing CO2 fixation together with increasing carbon flow towards metabolites. Interestingly, higher syngas H2 content favored ethanol and 2,3-butanediol production, while higher H2:CO uptake ratios increased total flux through the Wood-Ljungdahl pathway rather than selectively favoring reduced by-products. Our results are valuable for a better understanding of syngas composition effects on the acetogen biocatalyst and for process engineering towards optimizing gas fermentation performance. HighlightsO_LISyngas composition affects acetogen growth, gas uptake, and carbon distribution C_LIO_LIHigher H2:CO uptake ratios increase carbon flow through the Wood-Ljungdahl pathway C_LIO_LIHigher relative H2 uptake reduces CO2 loss and increases metabolite production C_LI

In liquid fermentation of filamentous fungi such as Aspergillus oryzae, increased broth viscosity and biomass adhesion to bioreactor surfaces remain major challenges. We previously developed a hyphal dispersion mutant lacking two hyphal adhesion factors, namely cell wall -1,3-glucan (AG) and biofilm galactosaminogalactan (GAG) (AG{Delta}-GAG{Delta} strain). The culture broth of the AG{Delta}-GAG{Delta} strain has low viscosity, which improves mixing and enzyme production. However, mycelia still extensively attach to bioreactor walls and downstream equipment, which impairs mixing and reduces product recovery. The hydrophobin RolA, a surface-active protein of A. oryzae, densely coats conidia and hyphae and contributes to cell surface hydrophobicity. In this study, we disrupted the rolA gene in AG{Delta}-GAG{Delta} (AG{Delta}-GAG{Delta}-{Delta}rolA strain) and evaluated the effects of this disruption on hyphal adhesion to the walls of culture vessels, enzyme production, and bioreactor performance. At the flask scale, the adhesion to glass surfaces was significantly reduced and recombinant enzyme activity was increased by 10%. Improved culture recovery at the end of fermentation further increased total enzyme yield. In a lab-scale stirred-tank bioreactor, both growth and enzyme production were increased. Scaling-up to a 200-L bioreactor showed reduced agitation power consumption while improving hydrodynamic properties. Fermentation of AG{Delta}-GAG{Delta}-{Delta}rolA was successfully scaled up to a 3000-L bioreactor; consistent enzyme activity and improved flow circulation in the bioreactors were confirmed by computational fluid dynamics analysis. Overall, the AG{Delta}-GAG{Delta}-{Delta}rolA strain has increased enzyme production and scalability, supporting its suitability for industrial applications.

Acetate is a promising carbon source for microbial biotechnology as it can be produced sustainably from lignocellulosic biomass or C1 gases. Since acetate is directly activated to acetyl-CoA, it is especially suitable for producing acetyl-CoA-derived products, showcased here with the production of 3-(3-hydroxyalkanoyloxy) alkanoic acids (HAAs). P. putida KT2440 can natively metabolize acetate, but the weak acid has also inhibitory effects on microbial growth. We present an in-depth study on the physiology of P. putida KT2440 using acetate as carbon and energy source and evaluate acetate as feedstock for the biosynthesis of HAAs. Initially, a rational engineering approach to overexpress acetyl-CoA synthetase for acetate activation resulted in an improved growth rate of 16% and reduced lag phase by six hours. To further increase the performance of P. putida KT2440 on acetate, adaptive laboratory evolution was performed. This resulted in an improvement in the growth rate from 0.4 h-1 to 0.6 h-1 and enabled growth on up to 12.5 g L-1 acetate with a shortened lag phase compared to the wild type. Whole-genome sequencing revealed mutations in proteins involved in gene expression regulation and signal transduction. This evolutionary engineering approach informed the deletions of gacS and crc, which resulted in a reduction in the lag phase from seven hours to one hour and an improvement of the growth rate by 25 %, matching the growth properties of the evolved clones. Using the evolved strains for the production of HAAs resulted in faster biomass and product formation with product titers reaching up to 94 % of that of the wild type. In conclusion, we identified mechanisms in the acetate metabolism of P. putida KT2440 and improved the growth performance of the strain by rational and evolutionary engineering, demonstrating the potential of the promising, but challenging 3rd generation feedstock acetate.

The pulp and paper industry produces large volumes of condensed kraft lignin, which is challenging to convert to single chemical products. For this purpose, tandem chemical depolymerization and bioconversion to a single atom-efficient product is a potentially promising strategy. In this study, we conducted copper-catalyzed oxidative depolymerization using pine-derived kraft lignin to generate multiple bioavailable aromatic monomers at a yield of 4.5 weight% (wt%; g monomers per g lignin) from both C--O and C--C bond cleavage, followed by counter-current extraction with a 52 wt% monomer recovery. This resulted in an oxidized lignin product containing vanillin, vanillate, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, 5-formylvanillin, 5-carboxyvanillin, 5-carboxyvanillate, acetovanillone, and vanillyl glyoxylate. Based on this stream composition, we engineered the industrially relevant soil bacterium Pseudomonas putida KT2440 to catabolize the latter five compounds via overexpression of ten heterologous genes (acvABCDEFSYK-6, vceABSYK-6, ligW2SYK-6, and mdlCPP). We combined these engineered pathways with previously reported strategies for muconate production from G- and H-type monomers to generate P. putida KMM428, which utilized 93.6 {+/-} 0.2 mol% of the quantified aromatic monomers in a depolymerized kraft lignin mixture, and produced muconate at a yield of 99 {+/-} 3 mol%, on a quantified monomer basis. Together, this work increases the theoretical carbon conversion efficiency of this process by 37.6 {+/-} 0.1 mol% through incorporation of three {beta}-5 cleavage products, in addition to traditional G-type monomers.

Basidiomycete fungi are an underexplored source of specialized metabolites with significant biotechnological potential. However, the environmental cues that activate their biosynthetic pathways remain poorly understood. Here, we investigated the response of the wood-decaying fungus Fomitopsis betulina, to nutritional competition using co-cultures with Escherichia coli. On solid medium, F. betulina inhibited the bacterial growth. Using a mass spectrometry-based metabolomics approach, we identified a Sumikis acid derivative, calcium diformate, and sulfuric acid among the compounds enriched within the inhibition zone and hypothesized that these compounds were associated with the acidification of the medium. Although F. betulina has previously been reported to produce the antibacterial compound piptamine, neither piptamine nor related derivatives were detected under our experimental conditions. In liquid medium, the co-culture with E. coli caused the rapid depletion of the available glucose, resulting in the establishment of carbon-starvation conditions and a 44% reduction in fungal biomass. Transcriptomic analyses revealed extensive metabolic reprogramming in response to bacterial competition, including the induction of genes involved in carbon acquisition, nutrient transport, redox homeostasis, and stress adaptation. Notably, a homolog of the Velvet regulatory complex, a central regulator of fungal development and specialized metabolism, was upregulated. The co-culture induced the expression of genes associated with multiple biosynthetic gene clusters, including terpene, polyketide, and fungal RiPP. Taken together, our results demonstrate that bacterial competition acts as a potent trigger of nutritional stress and secondary metabolism in F. betulina. More broadly, fungal-bacterial co-culture represents a promising alternative to extractions to identify high-value added metabolites pathways from basidiomycetes.

Glucoamylase is essential for industrial starch saccharification, but the limited thermostability and near-neutral pH tolerance of fungal glucoamylases necessitate cooling and acidification of liquefied starch. Here, we developed an artificial intelligence-guided strategy to simultaneously improve the thermostability, pH tolerance, and catalytic activity of glucoamylase from Penicillium oxalicum (PoGA). Two property-specific machine-learning models, CASPE-T and CASPE-A, identified substitutions associated with thermostability and pH tolerance, respectively. Experimental screening identified beneficial substitutions in 11 of 21 CASPE-T and 12 of 22 CASPE-A candidates. Folding-energy-guided recombination integrated the two traits while maintaining structural compatibility. The optimal variant, PoGA T513E/Q305N, exhibited 2.21-fold higher specific activity than the wild type, with half-life extended from 22.3 to 57.9 min at 60 degrees C and from 16.6 to 64.7 min at pH 8.0. Molecular dynamics simulations attributed these improvements to reinforcement of high-occupancy hydrogen-bonding networks, suppression of conformational fluctuations in the linker and carbohydrate-binding module, enhanced long-range dynamic coordination, and preservation of a compact catalytic architecture. At 60 degrees C and pH 6.5 without acidification, PoGA T513E/Q305N produced 219.9 g/L glucose and achieved 89.1% starch conversion, 31.4% higher than the wild type. This work provides an efficient framework for multi-objective enzyme engineering and sustainable starch biorefining.

Spices contain diverse plant secondary metabolites with antimicrobial and antioxidant activities that can influence plant-microbe interactions. Among these metabolites, curcumin and piperine are major bioactive constituents of turmeric and black pepper, respectively. In this study, we demonstrate that curcumin and piperine enhance alcoholic fermentation in the budding yeast Saccharomyces cerevisiae. Curcumin significantly promoted alcoholic fermentation under high-glucose conditions (20-40% glucose), which impose substantial osmotic stress on yeast cells. Under these conditions, curcumin enhanced yeast growth, improved osmotic stress tolerance, and increased resistance to cell wall digestion, suggesting enhanced stress adaptation during fermentation. Furthermore, deletion of HOG1, which encodes the central MAP kinase of the High-Osmolarity Glycerol (HOG) pathway responsible for the osmotic stress response, abolished the fermentation-enhancing effect of curcumin, indicating that Hog1 function is required for this effect. Consistent with this result, transcriptomic and RT-qPCR analyses revealed increased expression of stress adaptation-related genes, including known HOG pathway-responsive genes. In contrast, the expression of genes involved in amino acid catabolism was decreased at 12 h after the initiation of fermentation, while metabolomic analysis revealed increased intracellular levels of amino acids, including glutamate and asparagine, at 24 h. These coordinated transcriptional and metabolic changes are consistent with reduced amino acid catabolism and a shift toward a metabolic state favorable for sustained fermentation. Together, these findings suggest that curcumin enhances alcoholic fermentation under osmotic stress by promoting stress adaptation that supports yeast growth and sustained fermentation.

Lager is the most produced beer style world-wide and makes use of the bottom-fermenting hybrid yeast Saccharomyces pastorianus (S. cerevisiae x S. eubayanus). Previous research showed that flocculation in S. pastorianus, in contrast to the top-fermenting ale yeast S. cerevisiae, is triggered by nitrogen starvation. However, the cellular events leading to flocculation in S. pastorianus are not well characterized. Therefore, we conducted a proteomic screen of S. pastorianus TUM 34/70 and identified the protein kinase Ste20p and protein phosphatase regulatory subunit Ypi1p as higher abundant during flocculation. Overexpression of these genes caused a consistent and strong increase in flocculation rate over the complete duration of beer fermentation. Characterization of Ste20p and Ypi1p via a phospho-proteomics screen showed their targeting of proteins whose S. cerevisiae orthologues are involved in pseudohyphal growth. However, in contrast to this, the overexpression of STE20 and YPI1 led instead to the establishment of a flocculation morphology, giving first-time evidence that S. pastorianus repurposes the pseudohyphal signaling network for this phenotype.

Valerolactam is a promising bio-based monomer for polyamide synthesis, but microbial production remains limited by inefficient 5-aminovalerate (5AVA) cyclization, by-product formation, and insufficient process optimization. In this study, Corynebacterium glutamicum was engineered for valerolactam production by expression of davBA from Pseudomonas putida and lysP from Escherichia coli, followed by conversion of 5AVA to valerolactam using the recently identified avaC gene from Collinsella intestinalis. Flask cultivations confirmed efficient valerolactam formation with only minor accumulation of the by-products L-lysine, 5AVA, and glutarate. Batch bioreactor experiments showed that higher glucose concentrations increased titers but also promoted by-product accumulation, whereas increasing the dissolved oxygen setpoint from 30% to 50% improved growth and volumetric productivity. Intracellular cofactor analysis revealed declining energy status and shifts in redox balance during production. Based on these findings, carbon-limited fed-batch cultivation at 50% rDO improved production performance, reaching 3.6 g/L valerolactam with a yield of 0.231 g/g and a volumetric productivity of 0.075 g/L/h, while minimizing by-product formation. These results establish AvaC-based C. glutamicum as a promising platform for sustainable valerolactam biosynthesis.

Background: Hydroxyectoine is a high-value compatible solute with applications in cosmetics, healthcare, and biotechnology. Its microbial production has traditionally relied on halophilic organisms requiring high-salinity cultivation, motivating the development of non-halophilic production hosts. Corynebacterium glutamicum is an attractive platform because of its industrial robustness and high metabolic capacity through the aspartate-family amino acid pathway. Results: A synthetic hydroxyectoine pathway was constructed by combinatorially varying the predicted translation initiation rates of four translational units comprising ask, ectAB, ectC, and ectD. A library of C. glutamicum transformants was screened at 40{degrees}C using hydroxyectoine-associated thermoprotection as a functional selection principle. Fast-growing variants generally displayed increased hydroxyectoine formation and higher hydroxyectoine-to-ectoine ratios than a strain carrying the native pathway configuration. The selected combination reached a hydroxyectoine-to-ectoine ratio of 4.7 and was transferred into the lysine-producing strain DM1729SL in order to increase precursor availability and hydroxyectoine production. Carbon-limited fed-batch cultivations showed that both temperature and dissolved oxygen influenced production. The best performance was obtained at 30{degrees}C and 50% relative dissolved oxygen, yielding 12.9 g/L hydroxyectoine with a yield of 0.161 g/g glucose and a volumetric productivity of 0.26 g/L/h after glucose depletion. A subsequent hypoosmotic downshock increased extracellular hydroxyectoine recovery to 14.5 g/L. Conclusions: Thermal stress-based combinatorial pathway balancing enabled efficient de novo hydroxyectoine production in C. glutamicum. Integration of precursor-enhanced host metabolism, controlled oxygen supply, fed-batch cultivation, and osmotic downshock resulted in a substantial improvement over previously reported de novo hydroxyectoine production in this host and establishes C. glutamicum as a promising platform for further hydroxyectoine process development.

BackgroundMicrobial chain-elongation by Clostridium kluyveri using the products (acetate and ethanol) derived from the electrocatalytic CO2 reduction reaction (CO2RR) represents a unique sustainable strategy for producing C4-C6 chemicals from CO2. However, direct integration of electrocatalytic effluents with anaerobic bioprocesses is often impeded by the physiological incompatibility between electrocatalytic product streams and microbial metabolism. Specifically, CO2RR effluents commonly contain formate, which cannot be utilized by C. kluyveri for chain elongation and therefore reduces the overall carbon efficiency of CO2 conversion to C4-C6 chemicals. Moreover, both formate and the elevated phosphate concentrations typical of electrochemical reaction solutions may inhibit microbial growth. ResultsWe show that formate at concentrations of up to 50 mM did not inhibit the growth of or the chain elongation by C. kluyveri. Based on this finding, we developed a modular two-step bioprocess. In the first step, the acetogen Clostridium ljungdahlii converts formate in CO2RR product mixtures into acetate, thereby generating additional substrates for second-step C. kluyveri-driven chain elongation, thus increasing the CO2RR carbon-conversion efficiency to C- C6 chemicals. To address the issue of C. ljungdahliis inhibition by high phosphate concentrations in electrocatalytic solutions, we explored the use of C. ljungdahlii biofilms for the first, i.e. the formate-conversion, step. C. ljungdahlii biofilms exhibit tolerance to concentrated electrolytes, enabling the conversion of up to 50 mM formate in CO2RR solutions. ConclusionsThe demonstrated two-step process constitutes the basis for the development of a robust and carbon-efficient biological process for the scalable upgrading of C1-C2 CO2RR products into higher-value C4-C6 chemicals.

Synthetic allopolyploidization is a powerful strategy for generating strains with novel industrially relevant traits. During the design of select, hybridize, evolved and learn cycle, the mitochondrial inheritance is considered neutral and most studies overcome their phenotypic impact. Here, we generated 168 synthetic allotetraploid strains representing all pairwise parental combinations of eight wild Saccharomyces species, and systematically controlled mitochondrial inheritance in these crosses. These allopolyploids were phenotyped across 31 environmental conditions relevant to biotechnology. In ~50% of all condition-strain combinations conditions, allotetraploids exhibited mid-parent heterosis. In approximately 25% of conditions, we found crosses with hybrid vigor, particularly in combinations involving Saccharomyces arboricola x Saccharomyces mikatae . However, allotetraploids were highly unstable and rapidly sporulated. Our analyses revealed that environmental conditions accounted for the largest effects, follow by its interaction with mitotype. However, mitotype alone showed small effects but significantly affected 42% of the tested conditions, underscoring the importance of mitochondrial inheritance as a key determinant of allopolyploid performance. These findings demonstrate that mitochondrial inheritance is a key, environment-dependent determinant of allopolyploid fitness and should be considered alongside nuclear genome composition in the rational design of industrial allopolyploid strains

Methyl 12-aminododecanoate (ADAME) is a key precursor for Nylon 12 synthesis and an attractive target for sustainable microbial production. However, efficient biosynthesis of ADAME requires the coordinated oxidation and transamination of methyl dodecanoate (DAME), and identifying compatible enzymes for this multistep pathway remains challenging. In this study, we applied a machine learning-based bioinformatic screening approach to identify alternative enzymes for DAME-to-ADAME bioconversion. Among 18 selected distantly related AlkB homologs, AlkBGp01 from Alcanivorax sp. P2S70 showed activity toward DAME, producing 12-hydroxydodecanoic acid methyl ester (HDAME) and 12-oxododecanoic acid methyl ester (ODAME) despite low sequence identity to Pseudomonas putida AlkB. Further screening identified compatible redox partners, AlkG60 from the same species as AlkBGp01 and AlkTp04, whose combination with AlkBGp01 resulted in almost sixfold higher ODAME production than that achieved with P. putida AlkBFGJLT. ODAME production was further increased by more than threefold by conjugating these three newly identified proteins. The optimized single-plasmid system comprising conjugated AlkBGp01, AlkG60, and AlkTp04, together with AlaD and newly identified omega-transaminases EAV41574 produced 0.28 mM gDCW-1 ADAME, representing a 5.6-fold improvement over the previously reported P. putida AlkBFGJLT-based system with AlaD-CV2025. These results demonstrate that machine learning-guided enzyme discovery can identify functional distantly related homologs and compatible enzyme combinations for constructing efficient synthetic pathways. This study also highlights the importance of optimizing pathway architecture, including enzyme conjugation and plasmid configuration, for improving microbial production of bio-based monomer precursors.

Bacterial microcompartments (MCPs) are versatile proteinaceous organelles that compartmentalize metabolic pathways, offering promising scaffolds for synthetic biology and metabolic engineering. However, designing customized nanobioreactors requires distinguishing structurally indispensable shell proteins from those that can be modified or deleted to tune shell permeability without disrupting core organelle assembly. In this study, we performed a systematic biophysical and metabolic characterization of the hexameric shell protein PduU to evaluate its potential as a modular platform for synthetic organelle engineering. We tested whether deleting pduU or selectively truncating its N-terminal {beta}-barrel domain preserves shell assembly, metabolite flux, and intermediate confinement. Our results demonstrate that PduU modifications alter shell permeability while fully maintaining organelle structural integrity, monodispersity, and electrostatic colloidal stability. Crucially, this modulation in permeability redirects internal metabolic flux toward the energy-generating propionate pathway, resulting in elevated cell biomass and significantly increased yields of propionate, an economically vital industrial platform chemical. By establishing that PduU is a non-essential structural component whose modification tunes small-molecule flux, this work highlights PduU as a flexible locus for shell engineering, providing a scalable strategy for biomanufacturing of high-value bio-based products in tailor-made MCP nanobioreactors.

Ugba, a traditional alkaline-fermented condiment produced from African oil bean seeds (Pentaclethra macrophylla Benth.), remains poorly characterised at genome resolution. This study characterised a single spontaneous ugba fermentation using genome-resolved shotgun metagenomics across Early (0-24 h), Mid (48-96 h), and Late (120-144 h) composite stages. Thirty metagenome-assembled genomes (MAGs) were recovered and grouped according to their temporal abundance patterns. The Early-stage retained MAG population was dominated by Bacteroidota-associated MAGs, which exhibited the highest carbohydrate-active enzyme density and broad glycoside hydrolase repertoires, consistent with substantial genome-encoded potential for utilisation of the plant-derived seed matrix. The Mid stage showed marked restructuring of MAG composition, while Core and Late-associated MAGs increased towards fermentation maturation. Functional differentiation was also evident among Corynebacterium MAGs: C. nuruki encoded a complete urease system, whereas C. phoceense_A encoded glutamate dehydrogenase and nitrate-reduction genes. These stage-associated changes coincided with progressive alkalinisation from pH 7.15 to 8.01. Together, the results show that temporal restructuring of reconstructed microbial populations was accompanied by differentiation in genome-encoded functional potential. This study provides a genome-resolved characterisation of microbial composition and functional potential during spontaneous ugba fermentation and expands current understanding of the microbial organisation of this traditional African fermented food.

Polyhydroxyalkanoates (PHAs) are microbial polyesters that represent a sustainable alternative to fossil fuel-based plastics. These biodegradable polymers have properties similar to conventional plastics and can be produced from waste materials. The key enzyme in PHA synthesis is PHA synthase (PhaC) and despite its importance, only a few PhaCs from extremophilic microorganisms have been characterised in detail. Here we characterised PHA synthase enzyme from the thermophilic bacterium Caldimonas thermodepolymerans DSM15344, an attractive candidate for PHA production from lignocellulosic residues due to its unique properties such as utilisation of xylose-rich substrates and high PHA yields on this pentose sugar. PhaC was successfully expressed in the surrogate host E. coli BL21 (DE3) GOLD, purified to homogeneity and its enzymatic activity was confirmed in vitro. The optimal pH range and temperature were determined as 6.3-6.9 and 50 {degrees}C, respectively. The melting temperature of PhaC was detected at 57.83 {+/-} 0.04 {degrees}C and the enzyme storage stability was assessed. The tertiary structure, including the enzyme active site, was predicted using available bioinformatic tools and the predicted catalytic residues were supported by site-directed mutagenesis. This study represents the first biochemical characterisation of PHA synthase from C. thermodepolymerans, expanding the limited set of characterised thermophilic PhaC enzymes.

Romanian bors, a traditional fermented wheat bran beverage, is produced through spontaneous fermentation and represents a complex microbial ecosystem. Despite its cultural importance and presumed health benefits, its microbial ecology and functional potential remain poorly characterized. The present study aimed to elucidate the microbial community structure of bors and link it to functional traits relevant to fermentation performance and food functionality by integrating culture-independent sequencing with culture-dependent isolation and functional characterization. A total of 32 bors samples (12 commercial and 20 homemade) were analyzed. Amplicon-based sequencing revealed a microbiome dominated by lactic acid bacteria (LAB), with lactobacilli accounting for the majority of the bacterial communities and Lactobacillus amylolyticus being identified as the most prevalent and abundant species. The yeast communities were mainly composed of fermentative taxa, including Pichia kudriavzevii and Kluyveromyces marxianus. Lactobacillus amylolyticus and P. kudriavzevii were also the most frequently isolated species among bacteria and yeasts, respectively. These results highlighted a strong adaptation of the microbial isolates to starch-rich cereal substrates and underscored the central role of these microorganisms in wheat bran fermentation for bors production. Whereas the sequencing-based analyses showed no significant differences in overall diversity between the commercial and homemade bors samples, the cultivation-based results indicated a higher bacterial richness in the commercial products. Notably, the culture-dependent method captured substantially fewer taxa, highlighting the complementary nature of the two approaches. Of a total of 101 bacterial strains (88 LAB and 13 acetic acid bacteria) isolated, many exhibited rapid growth and strong acidification capacity, reaching pH values below 4.5 within 12 h. A functional screening revealed that 21 % of these strains displayed -amylase activity, 65 % phytase activity, and 50 % {beta}-glucosidase activity, highlighting their capacity to metabolize cereal substrates and enhance the nutrient availability of bors. All strains showed antibacterial activity against at least one indicator bacterium tested, with a universal inhibition of Listeria monocytogenes. Overall, Romanian bors harbored a lactic acid bacteria-dominated core microbiome with a significant functional diversity. These findings underscored its potential as a rich source of functional and technologically important strains for application in starter and protective culture development.

Myoglobin, an oxygen-binding animal protein, was engineered in Pisum sativum (pea) to explore its potential as a food ingredient and balance the amino acid profile. In this study, minimal expression cassettes and binary vectors were used to express bovine myoglobin using particle gun and Agrobacterium-mediated transformation, respectively. Successful integration and expression of the myoglobin gene was achieved in P. sativum, with both methods yielding similar transformation efficiencies (~1%). Expression analysis of T2 seeds revealed that Agrobacterium-mediated transformation-derived transgenic lines that expressed myoglobin under the regulation of a Soybean 7S seed-specific promoter and Tobacco Etch Virus (TEV) translation enhancer and a chimeric Rb7MAR Terminator (Ps-BpRG13 events) consistently yielded the highest level of expression (0.32-1.57% of TSP), while transgenic lines with myoglobin expression under the regulation of a Soybean Phaseolin promoter and Rb7MAR Terminator (Ps-BpRG14 events) resulted in moderate levels of heterologous protein expression (0.13-0.83% TSP). Transgenic events with constitutive 2xCaMV35S promoter, TEV translation enhancer and Rb7MAR terminator (Ps-BpRG15 events) exhibited the lowest level of myoglobin expression (0.09-0.14% TSP). Co-bombardment of two minimal expression cassettes - one with myoglobin under the regulation of the Phaseolin promoter and Rb7MAR Terminator and the other with the nptII selectable marker under the regulation of a 2X constitutive CaMV35S promoter, TEV translational enhancer and TNOS Terminator, yielded lines that exhibited variable expression (0.03-0.77% TSP), with some events comparable in expression to Agrobacterium-derived Ps-pRG14 events. To the best of our knowledge, this is the first report of producing a heme-containing animal protein, myoglobin, in peas, with potential implications for sustainable production of food ingredients and nutritionally fortified and value-added plant products using molecular farming.

Improving carbon recovery during sugar fermentation remains a major challenge because a substantial fraction of substrate carbon is lost as CO2 during central metabolism. To overcome this limitation, Clostridium sp. JS66 (JS66), an acetogen producing hexanoic acid from glucose, was subjected to adaptive laboratory evolution under CO2/H2 conditions to enhance H2-assisted CO2 reassimilation during glucose fermentation. The evolved strain, ALECO2, exhibited CO2 consumption without a lag phase under autotrophic conditions and reached a 9.5-fold higher CO2 uptake rate than JS66. Under fed-batch conditions, glucose-only fermentation yielded a carbon molar yield (Cmetabolite/Csugar, CM/CS) of 0.60, whereas H2 supplementation increased CM/CS to 0.91 and redirected carbon flux toward C6 products (hexanoic acid and hexanol), which accounted for 49% of total C_output. With additional CO2 supplementation, ALECO2 further assimilated externally supplied CO2, increasing the CM/CS to 1.10 and demonstrating carbon-negative fermentation. Assimilation of externally supplied CO2 further redirected carbon flux toward chain elongation, producing 7.14 g/L hexanoic acid and increasing the C6 carbon fraction to 57% of total C_output. Constraint-based flux analysis supported increased acetyl-CoA formation through the Wood-Ljungdahl pathway and enhanced flux toward reverse {beta}-oxidation under H2- and CO2/H2-supplemented conditions. Genome analysis identified mutations including genes encoding a putative HytB homolog and a LysR-type transcriptional regulator. These results establish ALECO2 as a promising evolved anaerobic non-photosynthetic (ANP) mixotrophy platform that links CO2 reassimilation and external CO2 assimilation with chain elongation, enabling carbon-neutral and carbon-negative production of value-added C6 products from glucose.

Synthetic microbial consortia have the potential to bring novel architectures to biotechnological processes. They enable more flexible and efficient bioprocesses by reducing metabolic burden and supporting division of labour. Obligately mutualistic cross-feeding has been used to stabilise the population composition of artificially assembled consortia. However, many current strategies rely on the cross-feeding of metabolites with limited exchange rates, and this imposes a growth burden on the consortium members. Here, we used adaptive laboratory evolution (ALE) to address this growth bottleneck and create an optimised co-culture chassis to host bioproduction functions. Transcriptome analysis revealed how ALE alleviated stress responses associated with nutritional restrictions in the non-evolved cross-feeding system. Using a case-study split bioproduction pathway, we demonstrated that improvements in the chassis growth performance resulted in production improvements, surpassing the performance of a monoculture implementation by 1.5-fold. Our results show the potential of ALE to optimise the cross-feeding layer of yeast co-cultures, and how this enables the efficient implementation of a bioproduction process.