Biotechnology for Biofuels最新文献

{"title":"QTL mapping, breeding, and debugging Saccharomyces cerevisiae strains through Reiterated Mass Selection and backcrosSing (ReMaSSing)","authors":"Lucas Souza de Bem,&nbsp;Joneclei Alves Barreto,&nbsp;Diego Trindade de Souza,&nbsp;Dione Oliveira Jordan,&nbsp;Sara Franchin Duarte de Souza,&nbsp;Danieli Canaver Marin,&nbsp;Josiel José Da Silva,&nbsp;Michel Brienzo,&nbsp;Leandro Vieira dos Santos,&nbsp;Sarita Cândida Rabelo,&nbsp;Gabriel Alves Margarido,&nbsp;Jeferson Gross,&nbsp;Ana Paula Jacobus","doi":"10.1186/s13068-026-02748-4","DOIUrl":"10.1186/s13068-026-02748-4","url":null,"abstract":"<div><h3>Background</h3><p>Producing second-generation ethanol from lignocellulosic hydrolysates (LCHs) poses significant challenges for <i>Saccharomyces cerevisiae</i> due to the presence of fermentation inhibitors. Quantitative trait loci (QTL) mapping of stress-tolerant <i>S. cerevisiae</i> strains is important for identifying adaptive alleles that can enhance yeast fermentation of LCHs. However, the QTL mapping process is labor-intensive, requiring the screening of numerous recombinants and repeated crossings to improve mapping resolution.</p><h3>Results</h3><p>We developed Reiterated Mass Selection and backcrosSing (ReMaSSing) to facilitate the identification of adaptive alleles through QTL mapping and to enhance LCH tolerance in yeast strains. ReMaSSing was applied to populations obtained by crossing the stress-resistant yeast PE-2_H4 with the laboratory strain S288C. Using alternative protocols, we selected haploid or diploid populations with dominant markers, enriching millions of segregants carrying adaptive alleles by propagating them in standard or LCH-supplemented media. The enriched pools were then bulk backcrossed with S288C, and germination of millions of spores generated new recombinant populations for subsequent selection cycles. After five rounds of ReMaSSing, whole-genome sequencing and QTL mapping identified key alleles associated with LCH tolerance, linked to <i>VPS70</i>, <i>CAT5</i>, <i>GCY1</i>, <i>UBP2</i>, <i>MKT1</i>/<i>SAL1</i>, <i>HAP1</i>, and <i>PHO84</i>, which influence growth and mitochondrial function in S288C. Mutations in <i>IRA1</i> and <i>HTA1</i>, unique to our S288C strain, were also mapped, highlighting ReMaSSing’s ability to “debug” the S288C background, i.e., to purge detrimental variants through selection. Allele swapping and competition assays confirmed that the identified QTL improved LCH tolerance and growth, with strains combining adaptive alleles performing over 20% better than the parental S288C. Finally, applying ReMaSSing to breed an LCH-tolerant yeast with a xylose-consuming strain produced recombinants with improved fermentation of xylose-enriched LCH.</p><h3>Conclusions</h3><p>ReMaSSing offers a practical protocol for generating QTL mapping populations to identify adaptive alleles in tolerant strains and correct genetic defects in inferior ones. Notably, recombinant populations and clones derived from ReMaSSing outperformed both parental strains in LCH tolerance and growth. Furthermore, we applied ReMaSSing to breed strains with enhanced LCH tolerance, efficient xylose catabolism, and robust ethanol production. Together, these results demonstrate that ReMaSSing is a powerful tool for engineering industrial yeast strains that integrate desirable traits from multiple parental backgrounds.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12997974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146183745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of a dockerin-containing expansin-like protein from the anaerobic fungus Neocallimastix californiae","authors":"Taru Koitto,&nbsp;Anna Pohto,&nbsp;Elizaveta Sidorova,&nbsp;Thu V. Vuong,&nbsp;Merja Penttilä,&nbsp;Emma R. Master","doi":"10.1186/s13068-026-02744-8","DOIUrl":"10.1186/s13068-026-02744-8","url":null,"abstract":"<div><h3>Background</h3><p>Anaerobic microbes produce multienzyme complexes known as cellulosomes to enhance the degradation of cellulosic substrates. These complexes localize diverse enzymes onto a protein scaffold, where proteins are anchored by dockerin domains. Although the cellulosomes of anaerobic fungi incorporate a broad array of cellulolytic enzymes, they remain largely unexplored. Notably, some fungal cellulosomes reportedly comprise expansin-like proteins with potential to disrupt cellulose networks. While two bacterial cellulosomal expansin-like proteins have been characterized, no fungal cellulosomal expansin-like proteins have been functionally characterized to date.</p><h3>Results</h3><p>Sequence analyses of expansin-like proteins from the anaerobic fungus <i>Neocallimastix californiae</i> revealed similar N-terminal domains among proteins with or without appended dockerins. Those without dockerins, however, consistently lacked the first conserved aromatic residue that forms the substrate binding surface of the C-terminal family 63 carbohydrate binding module. One cellulosomal expansin-like protein from <i>N. californiae</i> (<i>Nca</i>EXLX1) was recombinantly expressed with and without (<i>Nca</i>EXLX1tr) the dockerin domains. The adsorption characteristics of <i>Nca</i>EXLX1 and <i>Nca</i>EXLX1tr, and impact on cellulase (Cel7B) activity, were then investigated using quartz crystal microbalance with dissipation (QCM-D). <i>Nca</i>EXLX1 exhibited higher binding to cellulose nanofibrils (CNF) compared to <i>Nca</i>EXLX1tr. Despite the lower binding of <i>Nca</i>EXLX1tr to CNF, both <i>Nca</i>EXLX1 and <i>Nca</i>EXLX1tr enhanced the action of Cel7B to similar extents.</p><h3>Conclusions</h3><p>This study reports the production and characterization of a fungal cellulosomal expansin-like protein. The corresponding <i>Nca</i>EXLX1 protein and truncated variant were shown to enhance the activity of an endoglucanase, similar to observations made with non-cellulosomal expansin-like proteins. Notably, the improvement in cellulase activity upon the addition of <i>Nca</i>EXLX1 or <i>Nca</i>EXLX1tr was not correlated to extent of substrate binding.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1186/s13068-026-02744-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From beet molasses to malic acid: holistic development of fermentation and downstream process","authors":"Luca Antonia Grebe,&nbsp;Christina Maria Krekel,&nbsp;Constantin Alexander Maaß,&nbsp;Mario Beckers,&nbsp;Martin Smotrycki,&nbsp;An N. T. Phan,&nbsp;Lars M. Blank,&nbsp;Katharina Saur,&nbsp;Marcel Mann,&nbsp;Jörn Viell,&nbsp;Andreas Jupke,&nbsp;Jørgen Barsett Magnus","doi":"10.1186/s13068-026-02736-8","DOIUrl":"10.1186/s13068-026-02736-8","url":null,"abstract":"<div><h3>Background</h3><p>The growing demand for sustainable alternatives to fossil-based chemicals has increased interest in platform chemicals derived from renewable biomass sources, such as malic acid. This C4 dicarboxylic acid is valued for its diverse application potential in food, pharmaceuticals, and bioplastics. Sustainable platform chemicals remain commercially uncompetitive primarily due to high production costs driven by high substrate costs. Microbial production using more cost-effective feedstocks like sugar beet molasses shows promise. However, it faces challenges from high osmolality, growth inhibitors, and predetermined substrate composition during fermentation, as well as elevated pigmentation that complicates downstream processing. Moreover, the separation techniques typically used for highly polar carboxylic acids face considerable yield limitations due to the high solubility of malic acid and its salts.</p><h3>Results</h3><p>This study developed an all-encompassing production process for malic acid from untreated sugar beet molasses. Fermentative malic acid production with <i>Ustilago trichophora</i> was investigated in batch, fed-batch, and pulsed batch in shake flask scale, followed by a scale-up into 150 L pilot scale. A total of 15.7 kg malic acid was produced in a repeated pulsed batch with membrane-based cell retention with a titer of 108 g/L, a yield of 0.50 g/g, and a space–time yield of 0.66 g/L/h (max. 1.1 g/L/h). In addition, the byproduct succinic acid was detected in concentrations of up to 22.9 g/L. In the subsequent downstream processing, activated carbons were used for two-stage product capture, solvent change, and decolorization, followed by crystallization of the products malic acid and succinic acid. Based on experimental results, an Aspen Plus model was developed to estimate the overall process yields of 0.43 g malic acid (98% purity) and 0.10 g succinic acid per gram sucrose equivalent. A techno-economic analysis suggests production costs within the range of current market prices.</p><h3>Conclusion</h3><p>Agricultural residue streams are often proposed as cost-effective alternatives for fermentative platform chemical production, although the challenges addressed hamper the direct transfer of process strategies from established organic acid production. By presenting a holistic approach explicitly tailored to malic acid production from untreated molasses, this work demonstrates the techno-economic feasibility of the developed process at a meaningful scale.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12930559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioaugmentation in anaerobic digesters: a systematic review","authors":"Mozhdeh Alipoursarbani,&nbsp;Jeroen Tideman,&nbsp;Mitzy López,&nbsp;Christian Abendroth","doi":"10.1186/s13068-026-02746-6","DOIUrl":"10.1186/s13068-026-02746-6","url":null,"abstract":"<div><p>Bioaugmentation, the intentional introduction of specific microorganisms into anaerobic digestion (AD) systems, has shown promise in enhancing methane production and in mitigating stressful conditions, particularly in systems operating below optimal performance. This review presents a systematic literature review (SLR) of research on bioaugmentation in AD. This review identified and analysed studies meeting predefined eligibility criteria through a structured methodology involving research protocol, search, appraisal, synthesis, analysis, and reporting. A notable innovation of this review is its comprehensive critical comparison of different controls used in bioaugmentation studies, which has been inadequately addressed in previous literature. To facilitate the functional understanding, strains for bioaugmentation were grouped into the four phases of anaerobic digestion (hydrolysis, acidogenesis, acetogenesis and methanogenesis). A highly diverse set of microbes has been described for bioaugmentation, especially from the families <i>Clostridiaceae</i>, <i>Pseudomonadaceae</i> and <i>Syntrophomonadaceae</i>. Most works are related to hydrolysis. The few works that address acidogenesis are mostly related to dark fermentation. Several studies used methanogenic archaea as well as syntrophic acetate oxidising bacteria, despite the difficulties in culturing them. On the other hand, studies applying strains for acetogenesis were largely underrepresented. Especially works on syntrophic propionate and butyrate oxidation (SPO and SBO) were missing.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12930783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reliable renewable electricity generation system on small animal farms for rural electric vehicle charging","authors":"Meicai Xu,&nbsp;Carter Monson,&nbsp;Jacob Willsea,&nbsp;Sibel Uludag-Demirer,&nbsp;April Leytem,&nbsp;Barry Bradford,&nbsp;Wei Liao","doi":"10.1186/s13068-026-02745-7","DOIUrl":"10.1186/s13068-026-02745-7","url":null,"abstract":"<div><p>The adoption of electric vehicles (EVs) in rural areas is constrained by limited charging infrastructure, while small-scale dairy farms remain significant sources of greenhouse gas (GHG) emissions from manure management. This study addresses both challenges by demonstrating a dispatchable renewable electricity generation system that integrates anaerobic digestion (AD) with an external-combustion, Stirling-type combined heat and power (CHP) unit to support rural EV charging. A trailer-based system incorporating a 2.25 m³ AD reactor and a 5.6 kW CHP unit was constructed and operated using 28 kg/day of dairy manure. Results from a 50-day demonstration informed scaling and modeling for a representative 30-cow dairy farm. The AD process achieved a methane productivity of 232 L/kg volatile solids, with electrical and thermal conversion efficiencies of 15.05% and 37.11%, respectively. When scaled to a 30-cow farm, the system produced 46.46 kWh/day of net electricity and 10.43 kWh/day of recoverable heat, sufficient to meet realistic rural EV charging demands. Techno-economic analysis estimated a total capital investment of $99,000, annual operating costs of $2,000, and combined energy revenues of $7,797/year, corresponding to a 28-year payback period. Sensitivity analysis indicated that system economics are most strongly influenced by revenue generation. Life cycle assessment showed substantial environmental benefits relative to conventional manure management, including annual reductions of 324.44 tons CO₂-eq in global warming potential. Compared with stand-alone photovoltaic EV charging systems that require large battery storage to ensure winter reliability in northern climates, the biogas-based system leverages biogas storage as a low-cost energy buffer, enabling on-demand electricity generation with lower capital intensity. Overall, this work demonstrates a compact and scalable pathway for integrating manure-derived biogas with EV charging to advance rural electrification and circular bioeconomy goals.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12930540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and comparative genomic analysis of prophage sequences and CRISPR‒Cas immunity in Methylococcus genomes: insights into industrial methane bioconversion","authors":"Irina Nizovtseva,&nbsp;Alexey Rezaykin,&nbsp;Aleksandra Korenskaia,&nbsp;Maksim Zakhartsev,&nbsp;Alina Chigireva,&nbsp;Ilya Starodumov,&nbsp;Dmitrii Chernushkin","doi":"10.1186/s13068-026-02738-6","DOIUrl":"10.1186/s13068-026-02738-6","url":null,"abstract":"<div><h3>Background</h3><p><i>Methylococcus</i> species utilize methane as the sole carbon and energy source, converting it into biomass and other metabolic end products. Owing to this metabolic capacity, they hold particular promise in industrial C1 biotechnology, especially for the production of protein-rich feed. However, the industrial cultivation of <i>Methylococcus</i>-based consortia on methane is inherently nonsterile, exposing the process to potential biological risks that may compromise the stability, duration and productivity of cultivation. One of the most critical threats is bacteriophage infection, whose triggers for rapid phage-mediated lysis and resulting economic losses remain incompletely understood. Elucidating these processes is paramount for devising strategies to mitigate or prevent detrimental outcomes.</p><h3>Results</h3><p>In this investigation, nine publicly accessible genomes of <i>Methylococcus</i> species were examined, culminating in the identification of eleven prophage sequences distributed variably among the genomes. Sequence annotations revealed that nine prophages are potentially functional and intact, whereas the rest carry incomplete gene sets indicative of nonviability. Phylogenetic analyses corroborated the substantial diversity of prophages, which formed distinct clusters related to γ-proteobacteria phages. Furthermore, comparative genomic analyses demonstrated a high degree of structural conservation despite the presence of rearrangements. The annotation of the CRISPR‒Cas systems provided insights into additional dimensions of phage‒bacteria interactions. Examination of prophage integration sites did not reveal any disruption of metabolic gene structures, thus suggesting minimal risk of deleterious phenotypic outcomes.</p><h3>Conclusions</h3><p>These findings considerably advance the current understanding of the genetic diversity and biological properties of prophages infecting <i>Methylococcus</i> species, underscoring the importance of holistic approaches for the detection and analysis of these elements. Our findings underscore the need for routine prophage monitoring in industrial methanotrophic consortia, with the pipeline established here serving as a foundational framework for future refinement and industrial adaptation.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12924245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of an AA9 LPMO from Fusarium oxysporum and its role in cellulose hydrolysis and functionalization","authors":"Koar Chorozian,&nbsp;Maria Dimarogona,&nbsp;Marijana Ponjavic,&nbsp;Jasmina Nikodinovic-Runic,&nbsp;Evangelos Topakas,&nbsp;Anthi Karnaouri","doi":"10.1186/s13068-026-02742-w","DOIUrl":"10.1186/s13068-026-02742-w","url":null,"abstract":"<div><h3>Background</h3><p>Fungal AA9 lytic polysaccharide monooxygenases (LPMOs) play a central role in oxidative cellulose degradation and are key contributors to biomass conversion. While widely distributed in fungal genomes, many LPMOs remain uncharacterized, limiting our understanding of their functional diversity and biotechnological potential. <i>Fusarium oxysporum</i>, a genetically rich but underexplored species, contains several AA9 LPMOs. This study focuses on the characterization of one such enzyme named <i>Fo</i>LPMO9A, demonstrating its role in lignocellulose degradation and its potential for cellulose-based material functionalization.</p><h3>Results</h3><p>The gene encoding <i>Fo</i>LPMO9A was heterologously expressed in <i>Pichia pastoris</i>, and the produced recombinant protein was evaluated for its biochemical and functional properties, revealing C1/C4 regioselectivity on cellulosic substrates and higher H₂O₂ production compared to other AA9 fungal LPMOs. Its activity was assessed through the release of oxidized cello-oligosaccharides from various substrates and its synergistic action with cellulases. The stronger synergistic effect on lignocellulosic biomass likely reflects the enzyme’s ability to target complex, less accessible structures, where oxidative cleavage complements cellulase activity. Attention was given to how <i>Fo</i>LPMO9A responds to phenolic compounds and lignin-derived fractions, both in their native form and after enzymatic oxidation by redox enzymes such as laccases and polyphenol oxidases. In the case of lignin-derived fractions, the goal was to assess how these modifications influence their ability to drive <i>Fo</i>LPMO9A activity as redox-active electron donors. Building on its characterized activity, <i>Fo</i>LPMO9A was applied in two biotechnological contexts. First, it was integrated into a three-step enzymatic process for isolating micro-fibrillated cellulose from OxiOrganosolv-pretreated wheat straw. This treatment led to enhanced fibre disruption and finer fibrils, confirmed by determination of fibre diameter distribution, while fluorescence labelling with Rhodamine 110 verified C1-specific oxidation. Second, <i>Fo</i>LPMO9A was applied to bacterial nanocellulose produced by <i>Komagataeibacter medellinensis</i>, where successful oxidation and introduction of carboxyl groups were confirmed, demonstrating its potential to modify material properties.</p><h3>Conclusions</h3><p>This study underscores the versatile catalytic role of AA9 LPMOs in synergistic enzyme systems, emphasizing their impact on cellulose degradation and modification. The findings highlight the need for further exploration of LPMO mechanisms in biomaterial development and industrial applications.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12949506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147319270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Iron accumulation dynamics in Nostoc sp. PCC 7120: extent of biosorption in batch and continuous reactors","authors":"Veronica Lucato,&nbsp;Giulia Mazzola,&nbsp;Fengzheng Gao,&nbsp;Fabian Abiusi,&nbsp;Denis Badocco,&nbsp;Paolo Pastore,&nbsp;Alexander Mathys,&nbsp;Eleonora Sforza","doi":"10.1186/s13068-026-02743-9","DOIUrl":"10.1186/s13068-026-02743-9","url":null,"abstract":"<div><h3>Background</h3><p>Microalgae have recently gained attention for their ability to incorporate iron into organic molecules, potentially enhancing bioavailability and mitigating associated risks, suggesting a promising role in the field of iron supplementation. Among microalgal species, nitrogen-fixing organisms present a relatively high iron demand due to their unique metabolic requirements, positioning them as promising candidates for addressing iron deficiencies. However, information on the dynamics and extent of iron accumulation in diazotrophic cyanobacteria remains limited. Understanding how these organisms regulate iron uptake and storage under different cultivation conditions is essential to evaluate their potential for nutritional and biotechnological applications.</p><h3>Results</h3><p>This work investigates the iron accumulation dynamics of the diazotrophic species <i>Nostoc</i> sp. PCC 7120 under both batch and continuous systems. The results highlight its ability to adapt and survive across a wide range of iron concentration and demonstrate a strong correlation between iron availability and the internal quota of iron in biomass. High-density batch cultivation revealed that the iron content in <i>Nostoc</i> sp. can span a remarkably wide range, up to tens of thousands of mg_Fe kg_X⁻¹, far exceeding typical values reported in the literature. This high accumulation mainly results from consistent external biosorption of the metal onto the cell surface. In continuous steady-state culture, the externally biosorbed fraction was lower but still detectable, suggesting that adsorption substantially contributes to overall iron accumulation. Under strong iron limitation (below 0.5 mg_Fe L⁻¹), a marked increase in exopolysaccharide production was observed, suggesting that the extracellular matrix plays a functional role in the biosorption of the metal.</p><h3>Conclusions</h3><p><i>Nostoc</i> sp. PCC 7120 exhibits an exceptional capacity to tolerate and accumulate iron over a broad concentration range, mediated by both intracellular uptake and extracellular adsorption. These findings reveal that diazotrophic cyanobacteria can effectively modulate their iron management strategies under different regimes and highlight their potential as biofactories for iron-enriched biomass and as model systems for studying biologically driven metal sequestration.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12931063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147277754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis","authors":"Shi-Long Jin,&nbsp;Si-Yu Wei,&nbsp;Geng-Rong Gao,&nbsp;Lian-Bo Wei,&nbsp;Zhi-Xuan Li,&nbsp;Shao-Bo Zhang,&nbsp;Xin Liu,&nbsp;Xin-Hua Qi,&nbsp;Ming-Zhu Ding,&nbsp;Jing-Sheng Cheng,&nbsp;Yong Zhang","doi":"10.1186/s13068-025-02733-3","DOIUrl":"10.1186/s13068-025-02733-3","url":null,"abstract":"<div><h3>Background</h3><p>Artificial microbial consortium has been widely employed to improve the production of fengycin, a natural lipopeptide. Kinetic models are essential for understanding and predicting the dynamic behavior of metabolic systems, especially microbial consortia. Since the time evolution of metabolite concentrations and biomass is continuous and dynamic, systems of ordinary differential equations (ODEs) provide a natural and effective framework for capturing such interactions. In this work, a kinetic model based on ODEs was established to describe a multi-strain artificial consortium for fengycin synthesis, utilizing <i>Bacillus subtilis</i>, <i>Yarrowia lipolytica,</i> and <i>Corynebacterium glutamicum</i> as target strains.</p><h3>Results</h3><p>The model captures microbial growth, intermediate metabolite formation, final product synthesis, and substrate consumption. It was successfully applied to analyze and interpret the cultivation data of target strains on various substrates. The model explicitly incorporates the accumulation of amino acids synthesized by <i>C. glutamicum</i>, the accumulation of fatty acids synthesized by <i>Y. lipolytica</i>, and the process in which <i>B. subtilis</i> utilized amino acids and fatty acids as partial precursors for fengycin production. The mathematical model ended up as a nonlinear ordinary differential system, which was solved with an adaptive step-size Runge–Kutta method, coupled with a genetic algorithm to roughly estimate the optimal model parameters associated with cellular growth, substrate consumption, and product level in fermentation broths.</p><h3>Conclusions</h3><p>The numerical results of the kinetic model agreed well with experimental data, and all seven sets of experimental conditions were fitted with overall relative errors ranging from 7.4 to 15.1%. This kinetic modeling provided a meaningful tool for the rational design and construction of further artificial consortia.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12918404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146069445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated omics analysis of the cellulose co-degradation network of Chaetomium thermophilum","authors":"Xinran Yu,&nbsp;Su Ma,&nbsp;Xiuyun Wu,&nbsp;Lushan Wang","doi":"10.1186/s13068-026-02741-x","DOIUrl":"10.1186/s13068-026-02741-x","url":null,"abstract":"<div><h3>Background</h3><p>Efficient degradation of cellulose is a key bottleneck in the industrialization of biofuels. While fungi achieve substrate conversion through precise regulation of cellulase systems, the systematic mechanisms underlying efficient degradation (encompassing gene transcription, extracellular protein cooperation, and product metabolism) remain unclear in specific fungi, especially thermophilic fungi critical for industrial production.</p><h3>Results</h3><p>(1) <i>C. thermophilum</i> did not induce cellulases under cellobiose, while microcrystalline cellulose (MCC) strongly activated degradation. <i>Ct</i>Clr-2 acts as a core transcription factor, directly driving the co-expression of key genes including LPMOs, CDH, and CBH; its deletion reduces MCC degradation efficiency by 30%. (2) Enzyme secretion may follow a three-stage cascade pattern (CBH1-A → LPMOs/CDH-1 → CBH1/2-B), where the selective secretion and temporal synergy of oxidases and hydrolase increase the reducing sugar yield by 60.6%. (3) The sugar acid metabolic network may enable efficient utilization of degradation products and potentially help maintain extracellular pH.</p><h3>Conclusions</h3><p>This study reveals the efficient \"transcriptional regulation-enzyme secretion adaptation\" synergistic mechanism in <i>C. thermophilum</i>. <i>Ct</i>Clr-2 coordinates key genes, and staged enzyme secretion optimizes synergy, while sugar acid metabolism ensures homeostasis. These insights advance thermophilic cellulolysis understanding and provide targets for engineering industrial strains through synthetic biology (for example, enhancing enzyme yield and optimizing degradation efficiency), aiding cost reduction in biofuel production.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"19 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12911045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}