[object Object], [object Object]

Frontiers in Microbiology • 2026

3-Methyl-1-butanol (3MB), also known as isoamyl alcohol, is an emerging bio-based solvent, platform chemical, and advanced biofuel candidate whose demand continues to grow across chemical, energy, and consumer product sectors. Microbial synthesis offers a sustainable alternative to petrochemical routes, yet achieving industrially viable titers remains challenging due to pathway complexity, byproduct formation, redox imbalance, and product toxicity. This review provides a comprehensive summary of current advances in microbial 3MB production, including host strain and pathway engineering, feedstock diversification, and fermentation design. We compare the three principal biosynthetic routes toward 3MB—the valine–leucine–Ehrlich pathway, the mevalonate pathway, and the isovaleryl-CoA pathway—and evaluate their implementation across bacterial and yeast chassis. Particular focus is placed on strategies that enhance flux through leucine biosynthesis, reduce byproduct formation such as isobutanol, and rebalance NAD(P)H cofactors. Mechanisms of 3MB toxicity and recent insights from adaptive laboratory evolution and omics analyses are discussed as emerging guides for improving product tolerance. Beyond genetic interventions, we highlight process-level opportunities such as in situ product extraction, oxygen-supply optimization, and fed-batch operation, which remain underexplored yet are critical for achieving high 3MB titers. Looking forward, leveraging isobutanol chassis strains, employing high-throughput technologies such as biosensor-guided evolution, adopting intensified fermentation strategies, and co-producing 3MB alongside bioethanol may accelerate the development of scalable and economically competitive microbial platforms for 3MB production.

[object Object], [object Object], [object Object] et al.

Microorganisms • 2026

Behavioral maturation is essential for the proper functioning of honey bee societies and is regulated by multiple factors such as juvenile hormone (JH) and nutritional deficiency. Although recent studies have shown that surface-associated microbiota in insects can modulate host behavior, the relationship between body surface microbiota and behavioral maturation in honey bees remains largely unexplored. This study aimed to determine whether the surface microbial communities of honey bees shift with behavioral maturation. By using 16S rRNA gene amplicon sequencing, we analyzed the surface microbiota of worker bees at different behavioral stages (newly emerged bees, nurses, and foragers) in both Eastern honey bee Apis cerana and Western honey bee Apis mellifera. The results showed that in both honey bee species, nurse bees exhibited the lowest microbial diversity, while forager bees showed the highest, and newly emerged bees had an intermediate level of microbial diversity. Moreover, beta diversity analyses revealed that the body surface microbiota of worker bees significantly varied across behavioral stages in both bee species and differed between the two bee species at the same behavioral stage. Additionally, in both bee species, at the phylum level, Pseudomonadota, Bacillota, and Actinobacteriota dominated the worker bee body surface microbiota; at the genus level, foragers had more Gilliamella, while nurses harbored more Lactobacillus. Together, our findings reveal the emergence of distinct microbial signatures on honey bee body surfaces during behavioral maturation.

[object Object], [object Object], [object Object] et al.

Frontiers in Nutrition • 2026

The bioconversion of fish by-products has been evidenced as a sustainable process to convert food waste into high-value products. In the present study, protein hydrolysates were produced from fish by-products by different bioprocesses and evaluated as fertilizers in wheat ( Triticum aestivum L. ) on a nitrogen-equivalent basis. Fish by-products were processed through grinding prior to bioconversion. Enzymatic hydrolysis was performed using Alcalase at 55 °C, pH 6.5, and a 3-h reaction, while microbial conversion was assessed using a lactic culture at 40 °C, pH 6.5, and a 10-day culture. Hydrolysates obtained by enzymatic and microbial bioconversion were evaluated as fertilizers by adding 30 mg after 7 and 14 days to wheat seeds sown under controlled conditions. Protease and microbial hydrolysis generated high concentrations of α -amino groups, yielding 100 mM and 170 mM, respectively. The combined process exhibited a synergistic effect, yielding 226 mM of α -amino groups and 33% of protein recovery. Plant growth assays were conducted under controlled conditions using nitrogen-equivalent doses of each hydrolysate. Microbial and combined enzymatic-microbial hydrolysates generated average plant lengths of 52 cm and 54 cm compared to 44 cm in the control, while plant biomass reached 1.7 g and 2.3 g with microbial and combined enzymatic-microbial hydrolysates compared to 0.7 g in the control. Photosynthetic parameters remained within normal physiological ranges from 2.5 to 3.3 for performance index (PI) and from 0.78 to 0.80 for maximum quantum efficiency (Fv/Fm). The integration of enzymatic and microbial catalysis produced the most effective biostimulant activity, highlighting the value of combining enzymatic specificity with microbial metabolic versatility. These findings support fish-derived protein hydrolysates as efficient and eco-friendly fertilizers that are capable of improving plant growth while contributing to sustainable and integral utilization of natural resources.

[object Object], [object Object], [object Object] et al.

FEMS Microbiology Ecology • 2026

Abstract Accurate assessment of microbial community structure via high-throughput sequencing is fundamentally dependent on primer selection; however, systematic primer optimization for freshwater lake ecosystems remains insufficiently explored. Using the representative Lake Qiandao as a model, this study provides an integrative comparison of multiple primer sets targeting the 16S rRNA gene (V1-V2, V3-V4, V4, and V5-V7), the 18S rRNA gene (V4-1 and V4-6), and the Internal Transcribed Spacer (ITS1 and ITS2) regions. Our results elucidate that the V3-V4 region yielded significantly higher bacterial diversity and a more biologically representative community structure. For eukaryotic microorganisms, the V4-1 primers exhibited superior performance, capturing a broader taxonomic spectrum of algae (e.g. Ochrophyta and Cryptophyta) and protozoan groups. Regarding fungi, the ITS2 region provided enhanced stability and more comprehensive taxonomic coverage compared to ITS1. This study establishes a standardized molecular framework for microbial diversity research in freshwater limnology and underscores the necessity of primer optimization to ensure the high-fidelity resolution of microbial community structures and their associated ecological function.

[object Object], [object Object]

PLOS One • 2026

Protein-based gel matrices are increasingly explored for feed applications requiring soft or semi-solid formulations, but achieving strong gelation along with high water- and oil-holding capacities at low protein concentrations remains challenging. In this study, soy protein isolate (SPI) was modified via nitrogen-protected thermal induction followed by microbial transglutaminase (MTG) cross-linking to enhance its suitability as a gel-feed matrix. Single-factor and orthogonal experimental designs were used to investigate the effects of SPI concentration, MTG dosage, reaction temperature, reaction time, and pH on macroscopic gelation (measured as apparent viscosity), nitrogen solubility index (NSI), water-holding capacity (WHC), oil-holding capacity (OHC), and microstructure (SEM). Under optimized conditions—10% SPI, 0.3% MTG, 50 °C, 3 h, pH 7—gelation increased by approximately 373%, WHC improved by 222%, and OHC increased by 150%, while SEM confirmed the formation of a more regular three-dimensional network compared with native SPI. These results indicate that dual-modified SPI exhibits enhanced functional properties relevant to gel-feed formulations, providing a practical foundation for laboratory-scale process optimization. Further pilot-scale evaluation and biological validation are warranted to assess scalability, processing efficiency, and performance in target animal applications.

[object Object], [object Object], [object Object] et al.

mBio • 2026

ABSTRACT Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host’s impaired ability to oxidize TMA to trimethylamine- N -oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline trimethylamine-lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levels in vivo . These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities. IMPORTANCE Gut microbial metabolic activities play important roles in human health, prompting interest in the discovery of gut microbiome-targeted small molecule inhibitors as potential therapeutics. Anaerobic choline metabolism by the gut microbiome generates trimethylamine and its downstream metabolite trimethylamine- N -oxide (TMAO), which cause trimethylaminuria and are correlated with cardiometabolic diseases, respectively. Current strategies for modulating microbial metabolism with small molecule inhibitors typically require having a target enzyme. Here, we show that a growth-based phenotypic screen can identify inhibitors of choline metabolism with chemical scaffolds that are structurally distinct from choline and existing inhibitors. The resulting optimized compounds lower serum TMAO in gnotobiotic mice without significantly perturbing gut microbiome composition. This work highlights the potential of using phenotypic screening to rapidly discover additional inhibitors of microbial metabolic activities, which would accelerate mechanistic studies of the microbiome and deepen our understanding of disease biology from correlation to causation.

[object Object], [object Object], [object Object]

Research Square • 2026

Abstract Aims Azolla , a robust nitrogen (N)-fixing plant, can be efficiently and ecologically cultivated when incorporated into rice fields, while the mechanisms remain inadequately understood. This study systematically explored these mechanisms by assessing the effects of Azolla returning on soil nitrogen forms, ammonia volatilization, and microbial community responses across key rice growth stages. Methods The effects of Azolla incorporation were compared against rice monoculture and urea application at various stages of rice cultivation. The study monitored changes in soil nitrogen forms and ammonia volatilization. Furthermore, the response of the soil microbial community was examined, with a detailed analysis conducted during the grain-filling stage. Results Azolla returning significantly increased the content of total soil N, organic matter, available potassium and available phosphorus, while also elevating the soil pH. It substantially elevated ammonium nitrogen and microbial biomass nitrogen (peaking at grain-filling) compared to monoculture or urea, while significantly reducing nitrous oxide emissions, ammonia volatilization and maintaining nitrogen fertilizer content over time. Soil microbial community during the grain-filling stage indicated that urea fertilizer favored the enrichment of nitrifying bacteria ( Nitrospira and Nitrosomonas ) but also increased the abundance of pathogen Pseudomonas syringae . Azolla returning potentially reduced the abundance of pathogens while significantly promoting that of beneficial bacteria involved in N fixation and denitrification, including Azospirillum and Bacillus bataviensis . These enhanced soil nitrogen fixation and metabolic capacity. Conclusions This study is the first to track the dynamic characteristics and potential mechanisms behind the changes in nitrogen source during Azolla incorporation, a process that enhances soil fertility and reduces environmental emissions. It provides a theoretical foundation for the adoption of this sustainable practice.

[object Object], [object Object], [object Object] et al.

Journal of Berry Research • 2026

Background Lor whey cheese (LWC) is a nutritious dairy product. Cornelian cherry ( Cornus mas L.) is a fruit rich in phenolic compounds and anthocyanins. Functional foods with enhanced nutritional value can be developed using the cornelian cherry fruit. Objective The main aim of this study was to produce functional LWC enriched with antioxidants and phenolic compounds through the addition of cornelian cherry puree, and to investigate its quality properties. LWC samples were evaluated in terms of physicochemical, microbiological, and sensory properties, as well as shelf life. Methods Cranberries were mashed following heat treatment and added to LWC at different concentrations (3%, 5%, 7%, and 10% w/w). All sample groups were vacuum-packed and stored at +4 °C until the analysis days (1st, 3rd, 5th, 7th, and 10th days). On these days, microbiological analyses were performed to evaluate shelf life. In addition, antioxidant activity and total phenolic content were measured in the LWC samples. Results The addition of cornelian cherry to LWC resulted in a reduction in total viable count, psychrophilic bacteria, and yeast numbers, along with an increase in Enterobacteriaceae spp. counts. The cornelian cherry puree contributed to a “phenolic character,” referring to the presence of plant-derived antioxidant compounds measured as total phenolic content (mg GAE/100 g). These compounds were associated with increased antioxidant activity, particularly in the LC5 sample (1.7 mg GAE/100 g), where consistent antioxidant effects were observed across all concentrations. The addition of cornelian cherry puree did not lead to a statistically significant change in the shelf life of LWC (p   0.05). Conclusions This study demonstrated that the addition of cornelian cherry puree to LWC resulted in a functional food product with enhanced phenolic compound content and antioxidant capacity.

[object Object], [object Object], [object Object] et al.

Fermentation • 2026

Indigo dyeing is a traditional microbial fermentation process practiced worldwide using plants that produce indican, a precursor of indigo. In Okinawa Prefecture, Japan, indigo dyeing is traditionally performed using a muddy suspension containing indigo, prepared from Strobilanthes cusia. In this region, the addition of a fully fermented dye liquid, Tomodane, is believed to promote fermentation, although its microbial basis remains unclear. In this study, we developed a laboratory-scale indigo fermentation system with biological replication to investigate the effects of Tomodane supplementation on the dyeing intensity, bacterial community dynamics, and indigo particle size. Fermentation supplemented with Tomodane showed an earlier onset of fabric dyeing than fermentation without Tomodane. Microbial community analyses revealed that the bacterial communities in Tomodane-supplemented fermentation converged more rapidly toward a stable community structure. Additionally, bacterial taxa putatively associated with extracellular electron transfer (EET), a process relevant to indigo reduction, were more abundant in the bacterial community at earlier fermentation stages in the presence of Tomodane. Indigo particle size decreased more rapidly during Tomodane-supplemented fermentation, coinciding with an earlier dyeing onset. These results suggest that Tomodane facilitates indigo fermentation by facilitating the early establishment of a functionally competent microbial community capable of efficient indigo reduction.

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International Journal of Molecular Sciences • 2026

Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon–fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant–microbe partnerships for coupled soil–groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil–groundwater ecosystems.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

Pesticides are synthetic agrochemicals widely used to protect crops from pests and diseases; however, their limited biodegradability and indiscriminate application pose serious risks to non-target organisms, soil fertility, human health, and overall environmental sustainability. Conventional physical and chemical remediation strategies often fall short in restoring contaminated ecosystems, highlighting the urgent need for effective and sustainable pesticide mitigation approaches. In recent years, in situ bioremediation has emerged as a promising, eco-friendly, and cost-effective strategy for pesticide degradation in agricultural soils. Under favourable conditions, microorganisms utilise pesticides as sources of carbon, sulphur, and electrons, facilitating their breakdown through diverse metabolic pathways, with enzymatic degradation playing a central role in chemical transformation. Microbial consortia exhibit enhanced degradation efficiency by leveraging functional diversity and synergistic interactions among their microbial members. For instance, a consortium comprising Azospirillum , Cloacibacterium , and Ochrobacterium achieved 100% degradation of 50 mg L −1 glyphosate within 36 h. Advances in microbiome engineering have further expanded the scope of bioremediation by enabling the targeted manipulation of microbial communities to improve degradation specificity and performance. Notably, the recombined genomes of Psathyrella candolleana and Pseudomonas putida , generated through protoplast fusion, degraded 78.98% of pentachlorophenol in contaminated water. Additionally, engineering the rhizosphere with plant growth–promoting microorganisms, combined with microbial genetic modification, has demonstrated significant potential in enhancing pesticide degradation while simultaneously improving crop growth and productivity. Such integrative approaches represent a sustainable pathway towards resilient agroecosystems. This review synthesises current knowledge on the impacts of pesticides on crop physiology and metabolism, explores conventional and advanced microbe-mediated degradation strategies, and highlights the role of microbial engineering and consortia-based systems. Furthermore, it discusses emerging technologies, environmental and economic benefits, and recent patentable innovations, underscoring their relevance for sustainable agriculture and ecological restoration.

[object Object], [object Object], [object Object] et al.

Wellcome Open Research • 2026

We present a genome assembly from an individual Halichondria panicea (bread-crumb sponge; Porifera; Demospongiae; Suberitida; Halichondriidae). The genome sequence has a total length of 131.46 megabases. Most of the assembly (99.62%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.57 kilobases. Gene annotation of this assembly by Ensembl identified 26 096 protein-coding genes. Five medium-quality bacterial bins were also recovered, of which three belonged to the main Amylibacter -related symbiont, termed Halichondribacter symbioticus .

[object Object], [object Object], [object Object] et al.

Translational Animal Science • 2026

Lay Summary Essential oils have been explored in livestock production as a natural antimicrobial to improve overall animal health and performance. This study investigated the effects of supplementing Agolin® Pig, a combination of micro-encapsulated essential oils, in late gestation and lactating sow diets on various aspects of sow and piglet performance during lactation, as well as the sow fecal microbiota. Twenty-five sows were blocked by parity and allotted into one of two treatment groups: 1) Agolin® Pig supplementation (AGO) at 200 ppm for two weeks before farrowing, during farrowing, and throughout lactation, or 2) no supplementation as a control (CON). All diets met standard nutritional requirements. The parameters measured were sow feed intake, body condition, milk composition, piglet growth performance, and sow fecal microbiota. Results indicated that AGO did not significantly affect sow feed intake, piglet growth, or colostrum and milk composition throughout lactation. However, sows fed AGO during lactation maintained body condition as measured by the Knauer Caliper, an objective tool to standardize sow body condition. There were slight changes in sow fecal microbiota diversity between the groups post-farrowing. This study suggests that Agolin® Pig may help maintain sow body condition during lactation and influence sow fecal microbiota.

[object Object], [object Object], [object Object] et al.

Research Square • 2026

Abstract Background: The human oral cavity harbours a diverse microbial community that influences both oral and systemic health. Disruption of this microbial balance can result in dental conditions such as tooth decay. University students are particularly at risk due to poor dietary habits and inconsistent oral hygiene. This study investigated the distribution of oral microbial flora and their association with tooth decay among students of a private tertiary institution in Nigeria. Methods: Oral swab samples were collected and cultured using standard microbiological techniques, including growth on chocolate, blood, and MacConkey agars for bacterial isolation, and Sabouraud agar for fungal isolation, and biochemical tests were performed for identification. A structured questionnaire assessed oral hygiene practices, sweet consumption, and oral health status. Data were analyzed using descriptive statistics, Chi-square tests, and binary logistic regression to identify variables. Results: The predominant microbial isolates were Streptococcus mutans (25%), Staphylococcus aureus (17%), Streptococcus sanguinis (12%), and Candida albicans (10%). Tooth decay was reported by 52% of participants and was significantly associated with S. mutans (p   0.001), S. aureus (p = 0.006), C. albicans (p = 0.001), and S. sanguinis (p = 0.031). These microorganisms also increased the odds of tooth decay, with odds ratios (OR) of 3.27(95% CI = 1.77–6.05), 2.08(95% CI = 1.23–3.52), 1.95(95% CI = 1.06–3.58), and 2.51(95% CI = 1.40–4.50) respectively (p   0.05). Furthermore, sweet consumption showed a significant positive correlation with tooth decay (p   0.001). Conclusion: Streptococcus mutans , S. aureus, S. sanguinis , and Candida albicans were strongly associated with tooth decay and high sugar intake was a key risk factor.

[object Object], [object Object], [object Object]

PeerJ • 2026

Fermented shrimp paste (Kapi) is a culturally significant condiment valued for its flavor and nutritional value. However, inconsistent production practices may lead to microbial contamination and histamine accumulation, posing health risks. Understanding microbial diversity, salt-tolerant pathogens, and the effectiveness of hygienic controls is essential for improving product safety and quality consistency. This study assessed the microbial and physicochemical characteristics of seven Kapi produced under varying hygienic conditions: a certified commercial export product (M1), a traditionally fermented product using 25% (w/w) salt (M2), wet-market bulk products (M3, M4), and sealed community-enterprise products (M5, M6, M7). Microbiological hazards were characterized using Oxford Nanopore sequencing, and physicochemical analyses, including histamine content, were conducted. M1 exhibited the highest safety and quality, with no detected pathogens. In contrast, M3 and M5 contained high microbial loads, including Staphylococcus aureus , Bacillus cereus , Clostridium perfringens , and fungi. Bacterial diversity varied significantly across samples, with M3 and M4 showing the greatest richness, whereas M6 had the lowest. Dominant species identified were Lentibacillus salinarum , Lentibacillus amyloliquefaciens , and Lentibacillus kimchi in M1, M3, and M4, and Staphylococcus sciuri in M2, M5, and M6, all of which possessed histamine-degrading potential. Alkalibacterium kapii dominated M7, while histamine-producing Jeotgalicoccus halotolerans was found in M5–M7. Physicochemical variations corresponded with production practices. M6 showed the highest histamine level (39.4 mg/kg), while M1 and M4 had the lowest (12.7 and 9.5 mg/kg, respectively), indicating differences in hygiene and salt management. Overall, microbial and physicochemical hazard levels were closely associated with production environments. To enhance the safety and consistency of Kapi, we propose a risk-based framework that includes standardizing salt concentration (25% w/w) to control microbial dynamics and histamine formation, strengthening hygienic practices from Good Hygiene Practice (GHP) to Good Manufacturing Practices (GMP) compliance to ensure adequate safety control, and applying defined starter cultures to stabilize fermentation and reduce variability. These strategies collectively address how hygiene, salt concentration, and environmental control influence microbial and physicochemical hazards in traditional fermented shrimp paste.

[object Object], [object Object], [object Object] et al.

Research Square • 2026

Abstract Aims Extracellular enzyme stoichiometry is a key indicator for assessing resource limitations faced by soil microorganisms. Yet the characteristics of microbial resource limitation in rhizosphere soil under the combined agricultural practices of intercropping and straw retention remain unclear. Methods Here, we conducted a field experiment in the black soil region of Northeast China, to quantify the effects of intercropping and straw retention on soil nutrients, microbial biomass, extracellular enzyme activities, and their C:N:P stoichiometry in the rhizosphere of maize and peanut crops. Results Our results revealed an average vector length (VL) of 1.68 and 1.57 for extracellular enzymes in the rhizosphere soil of maize and peanut, with a vector angle (VA) of 37.80° and 34.67°, respectively. This indicated that soil microorganisms in the rhizosphere of both crops were co-limited by C and N, and the N limitation was more significant in the peanut rhizosphere. Notably, the combined treatment of intercropping and full straw retention increased the VA by 5°, effectively alleviating N limitation in the rhizosphere soil. The extracellular enzyme C:N:P stoichiometry in the rhizosphere soil of maize and peanut was 1.33:1.29:1.00 and 0.89:1.29:1.00, respectively. Microbial biomass nitrogen (MBN) was the primary factor affecting microbial nutrient limitation. Conclusions The extracellular enzyme stoichiometric characteristics of rhizosphere soil differed significantly between the two crops. Intercropping had a stronger impact on rhizosphere microbial nutrient limitation than straw retention, and their synergistic effect could significantly alleviate rhizosphere microbial N limitation by enhancing extracellular enzyme activity.

[object Object], [object Object], [object Object] et al.

Microbial Genomics • 2026

Klebsiella aerogenes is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission dynamics and resistance mechanisms of clinical K. aerogenes in Albuquerque, New Mexico. We sequenced 177 clinical isolates collected between 2021 and 2023. We also developed a novel, species-specific PopPUNK database to facilitate rapid, high-resolution typing. The New Mexico K. aerogenes population was diverse but dominated by two global pandemic lineages, ST93 (47.5%) and ST4 (7.9%), which were significantly enriched for the virulence factors yersiniabactin and colibactin. Genomic evidence for recent local transmission was rare, with only four putative transmission pairs identified. The resistome was characterized by intrinsic and adaptive mutations. Nearly all isolates possessed gyrA mutations associated with decreased fluoroquinolone susceptibility. Mutations in the AmpC regulator AmpD and the outer membrane porin Omp36 were common, particularly within the dominant ST93 lineage. These mutations have been associated with increased AmpC-mediated carbapenem resistance. Our findings underscore the critical importance of genomic surveillance to monitor the transmission and evolution of adaptive resistance.

[object Object], [object Object], [object Object] et al.

Frontiers in Plant Science • 2026

Saline-alkali soils are widespread in ecologically fragile regions and are characterized by high salinity and alkalinity, leading to soil degradation and reduced productivity. To evaluate the potential of Arundo donax cv. Lvzhou No.1 for improving coastal saline-alkali soils, this study was conducted on Pingtan Island, Fujian Province, China. Three treatments were established: a blank control (CK), rhizosphere soils from one-year cultivation (R1), and five-year cultivation (R5). Soil physicochemical properties and microbial community structure were assessed using soil chemical analyses and high-throughput sequencing. Cultivation of A. donax cv. Lvzhou No.1 alleviated saline-alkali stress by reducing soil pH and salinity, with stronger effects under long-term cultivation. Soil fertility increased markedly, with organic matter (OM) and total nitrogen (TN) rising by 91.00% and 70.00%, respectively. Microbial diversity also increased, with fungal communities dominated by Ascomycota and bacterial communities by Proteobacteria. Functional predictions showed higher abundances of saprophytic genera ( Acremonium, Fusarium ) and enhanced bacterial metabolic pathways, including fatty acid synthesis and the tricarboxylic acid cycle, indicating increased microbial metabolic activity. These changes promoted organic matter turnover and nutrient release. Canonical correspondence analysis identified OM, TN, available nitrogen (AN), and available phosphorus (AP) as the primary drivers shaping microbial community structure. Overall, long-term cultivation of A. donax cv. Lvzhou No.1 improves coastal saline-alkali soils by enhancing physicochemical properties and optimizing microbial community composition. These findings provide a scientific basis for ecological restoration and sustainable utilization of coastal saline-alkali lands.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

Introduction Euphorbia jolkinii Boiss. is a native invasive weed. Its invasion altered microbial composition, total nitrogen (TN) and available nitrogen (AN). However, the mechanisms influencing N transformation remain unclear. Particularly, the roles of the microbiome and genes in mediating N transformations to facilitate E. jolkinii invasion remain poorly understood. Therefore, the primary objectives of this study were to evaluate how E. jolkinii invasion affects N transformation, microbial interactions, and key genes associated with AN accumulation. Methods We compared three patches (non-invaded, lightly, and heavily invaded patches of E. jolkinii ) by analyzing rhizosphere soils of E. jolkinii and Poa crymophila Keng. Integrating soil physicochemical indices with metagenomic sequencing, we investigated the relationships among microbial communities, gene abundance, and N transformation. Results With E. jolkinii increasing invasion intensity, N accumulation and transformation rates were significantly reduced in the rhizosphere of P. crymophila but enhanced in that of E. jolkinii , particularly for AN. Metagenomic analysis revealed that the invasion and expansion of E. jolkinii promoted functional adaptation of the microbial community, particularly by enriching the N cycling-related genes and increasing their relative abundance in the rhizosphere soil of E. jolkinii . Moreover, it inhibited the accumulation of N transformation functional genes in the rhizosphere soil of the companion plant, P. crymophila . Structural equation modeling identified Nitrospirota, Edaphobacter , Anaeromyxobacter , and soil N transformation rates as key drivers of AN accumulation. Discussion E. jolkinii facilitated N accumulation in its rhizosphere by modulating N-transforming microbes and key functional genes, underscoring one of its invasive advantages.

[object Object], [object Object], [object Object] et al.

Microbiology Spectrum • 2026

ABSTRACT Methane (CH 4 ) emissions from flooded paddy fields, exacerbated by excessive nitrogen (N) fertilizer application, trigger serious climate challenges. The impact of reducing N fertilization rate combined with iron (Fe) amendment on CH 4 emissions remains unclear. This 4-year field study (2020–2023) investigated the effects of 100%, 80%, 60%, and 0% of the conventional N (urea and commercial organic manure) fertilization rate (100%N, 80%N, 60%N, and 0%N) as well as 80%, 60%, and 0% of the conventional N with the Fe powder (≥99% purity) amendment (80%N + Fe, 60%N + Fe, and 0%N + Fe) on CH 4 emissions from subtropical rice paddies. The results revealed that 60%N + Fe treatments decreased cumulative CH 4 emissions by 43.79% compared to the non-amended treatment, and by 57.33% in relative to the 100%N treatment in the 2023 rice season ( P 0.05). Meanwhile, Fe amendment significantly lowered the mcrA / pmoA ratio, which facilitated the decrease in CH 4 emissions. Community assembly analysis showed that Fe amendment enhanced stochastic processes in methanogens at 60% of conventional N but reduced dispersal at 80% of conventional N, with opposite trends for methanotrophs. Co-occurrence networks demonstrated increased connectivity and reduced modularity under Fe amendment. Moreover, soil Fe 2+ content and methanogen community structure, as critical drivers, were negatively correlated with CH 4 flux and cumulative emissions ( P 0.05). Taken together, Fe amendment is a potent strategy to mitigate CH 4 emissions under reduced N fertilization, offering a green production solution for global paddy systems. IMPORTANCE This study clarified the effects of Fe amendment on CH 4 emissions from subtropical paddy fields under various N fertilization rates through a 4-year in situ field experiment. We found that the Fe amendment combined with reduced N fertilization rates decreased CH 4 emissions, in particular under the 60% of conventional N fertilization rate. Furthermore, the Fe amendment lowered the mcrA / pmoA ratio. Moreover, the Fe amendment increased connectivity while reducing modularity in co-occurrence networks of methanogen communities. Soil Fe 2+ content and methanogen community structure were key drivers of CH 4 emissions. The findings provide an insight into the microbial mechanisms of mitigating CH 4 emission from flooded paddy soils through the Fe amendment.

[object Object], [object Object], [object Object] et al.

mSphere • 2026

ABSTRACT The diversity in foraging behavior observed among species is indicative of their ability to adapt to specific environmental conditions, with dietary differences playing a crucial role in shaping the composition of gut microbiota. However, there are limited reports on the dietary habits and gut microbiota of François' langur ( Trachypithecus francoisi ) across different wild geographical populations. To address this, our study employed DNA metabarcoding and 16S rRNA sequencing to investigate variations in dietary composition and their influence on gut microbiota among distinct wild populations of François' langur, as well as among different groups within the same region. The dietary analysis revealed a broad diet, identifying 134 families and 336 genera of plants. The habitat quadrat survey results indicate significant differences in the habitats of François' langurs across different geographic populations. However, the dietary composition analysis reveals that while the food composition of different groups within the same region is relatively similar, there are notable differences across geographically distinct regions. The microbial community analysis demonstrated distinct compositional and structural divergence in gut microbiota between these populations, whereas no significant microbial differences were detected among groups within the same region. Further correlation analysis between diet and microbiota indicated that dominant plant taxa in the diet exhibited significant associations with Firmicutes, Proteobacteria, and other microbial phyla, displaying varying degrees of positive or negative correlations. This study elucidates how dietary variations among geographically distinct populations of François' langur drive changes in gut microbiota, reflecting their adaptive responses to local habitats. These findings provide valuable insights for the conservation management of François' langur populations and potential applications in health status monitoring. IMPORTANCE Understanding the mechanisms by which animals adapt to their environment is essential for effective conservation efforts. This study examines the endangered François' langur, focusing on the largely unexplored relationship between its dietary habits and gut microbiota across various wild populations. Our research indicates that although habitat vegetation varies significantly even among groups within the same region, their diets remain similar. Conversely, langur populations from distinct geographic areas exhibit notable dietary differences. These dietary variations, in turn, lead to distinct compositional differences in their gut bacterial communities. This diet-microbiome interaction serves as a crucial physiological indicator of how these primates adapt to their local forest environments. By illustrating that gut microbiota composition reflects an animal’s ecological response to its environment, this study offers a powerful and non-invasive tool for conservation. These findings are critical for developing targeted strategies, such as habitat restoration, and for monitoring the health of these rare primates through gut microbiome analysis.

[object Object], [object Object], [object Object]

• 2026

This protocol covers sample collection and analysis of microbial composition from lake water.

[object Object], [object Object], [object Object] et al.

Agronomy • 2026

Sustainable care of urban lawns requires methods that maintain high turf quality while reducing the use of chemical fertilizers. The objective of this three-year field study was to evaluate whether microbial inoculants can complement or partially substitute conventional fertilization (65–190 kg N·ha−1, 33–35.2 kg P·ha−1, and 124.5 kg K·ha−1) required to maintain high turf quality in an intensively managed lawn system. The experiment was conducted in Poland on a degraded chernozem, classified as Haplic Phaeozem. A standard mixture of perennial ryegrass and fescue was evaluated under four treatments: (1) untreated control; three commercial microbial formulations: (2) StymGrass P+K, containing nutrient-solubilizing Bacillus spp.; (3) BioVitaGrass, combining Bacillus spp. with arbuscular mycorrhizal fungi (AMF); and (4) NitroGrass, containing nitrogen-fixing Azotobacter spp. with Bacillus spp. All microbial treatments improved lawn quality compared with the untreated control. Lawns receiving BioVitaGrass or NitroGrass showed the strongest responses, including denser plant cover, greener and finer leaves, reduced disease symptoms, and increased concentrations of nutrients in the plant tissue. StymGrass P+K produced smaller but still positive effects. Measurements of plant conditions, such as leaf greenness and canopy development, also indicated improved photosynthetic activity in inoculated plots. These results support the role of plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi in nutrient mobilization, root stimulation, and stress resilience. Although most evidence comes from crops, this study provides novel field-based confirmation of multi-functional microbial inoculant efficacy in turfgrass under this study’s conditions.

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Research Square • 2026

Abstract Background: Coastal salt marshes of the northeastern United States have experienced major compositional shifts due to invasive species. While previous research has shown that these invasions impact microbial composition and nutrient dynamics, a significant knowledge gap remains regarding taxonomic and biochemical changes. This study investigated the effects of invasive Phragmites australis on soil chemistry and microbial community structure in the Quinnipiac River salt marsh in southern Connecticut, comparing invaded zones to areas dominated by the native foundation species, Sporobolus alterniflorus (formerly Spartina alterniflora ). We employed 16S rRNA sequencing to characterize microbial taxa and measured soil organic carbon (SOC), total nitrogen (TN), carbon-to-nitrogen (C:N) ratio, as well as environmental variables. Results: Our findings reveal that although mean TN and SOC stocks did not differ significantly between native and non-native dominated areas, there were spatial and temporal distinctions in soil chemistry and microbial assemblages. Sporobolus soils had a significantly greater C:N ratio, which may favor slower organic matter decomposition leading to greater capacity for carbon sequestration. In contrast, Phragmites soils, with higher pH and bulk density, could support more copiotrophic microbial taxa. Microbial community structure showed a significant separation between the two vegetation types at all taxonomic levels, with plant type explaining between 9.1 and 13.5% of the community variation. While Sporobolus soils had greater diversity at broader taxonomic levels, Phragmites soils supported more diversity from Family to Genus levels. Conclusions: These results underscore the role of vegetation in shaping microbial ecology and soil function, providing crucial insights for the management and restoration of salt marsh ecosystems.

[object Object], [object Object], [object Object] et al.

Wellcome Open Research • 2026

We present a genome assembly from an individual Osedax fenrisi (bone-eating worm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 699.06 megabases. Most of the assembly (96.07%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 20.29 kilobases. Gene annotation of this assembly by Ensembl identified 12 909 protein-coding genes. From the metagenome data, we recovered 11 bins, of which four were high-quality MAGs. The genomic data will provide a foundation for studying symbiotic nutrient acquisition, bone-degradation mechanisms, and the ecological roles of bone-eating worms in deep-sea carbon and nitrogen cycling.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

This study compares how system design and experimental conditions shape bacterial communities across distinct habitats in a coupled seawater aquaponic system and a marine RAS, and explores their functional implications for system efficiency and productivity. Bacterial communities from fish guts, biofilters, biofilms and water were characterized after 4 months of rearing flathead grey mullet ( Mugil cephalus ) and glasswort ( Salicornia patula ) using 16S rRNA gene sequencing. In the RAS, bacterial richness (Chao1 and ACE) and diversity (Shannon and Simpson) progressively increased across compartments, while they remained stable in the aquaponic system, likely due to the differences in system design such as UV filtration in the RAS. Significant differences in bacterial community structure (weighted UniFrac) and composition were found in the four habitat types compared between systems, reflecting the different design and functionality of each system. In particular, fish gut bacteria were typical teleost commensals associated with positive gut health and disease resistance, dominated by the phylum Pseudomonadota and the genus Pseudomonas but showing differences in lower abundant taxa between systems. The biofilm and water of the aquaponic system showed genera with plant growth-promoting, disease-resistance and nutrient-cycling properties, at higher abundances than in the RAS ( Mycobacterium, Sulfitobacter, Marivita, Fuerstiella, Blastopirellula, Hoeflea ). Furthermore, the balance of nitrifying ( i.e., Nitrosomonas ) and denitrifying bacteria ( Pseudomonas, Blastopirellula ) in the biofilters of both systems supported efficient nitrogen cycling and water quality maintenance. Collectively, these results demonstrate that microbial assembly in aquaculture systems is governed by system design and habitat type, with potential functional consequences for fish gut health, plant growth, and overall system efficiency, highlighting the promise of integrated marine systems as sustainable food production strategies.

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Environments • 2026

This study explores the physicochemical properties and microbiological community structure of oil-contaminated soils from Midrand and Roodepoort, South Africa. Due to sample pooling, the analysis provides a composite profile for investigating site-specific microbial adaptations rather than replicated ecological inference. The soils of Midrand exhibited acidity (pH around 5.5–5.9), elevated levels of heavy metals (e.g., Zn exceeding 1000 mg/kg), and the presence of 5–6 ring polycyclic aromatic hydrocarbons (PAHs). The soils in Roodepoort exhibited a near-neutral pH (about 6.2–7.2), characterized by specific metal concentrations (e.g., Cr exceeding 150 mg/kg) and an elevated presence of four-ring polycyclic aromatic hydrocarbons (PAHs). Metagenomic analysis indicated distinct microbial communities: Pseudomonas spp. were prevalent in Midrand, while Bacillus spp. were dominant in Roodepoort. Correlation analysis suggested connections between pollutants and microbial taxa; however, these findings are tentative. Recovered metagenome-assembled genomes (MAGs) indicated genetic potential for polycyclic aromatic hydrocarbon (PAH) degradation in Midrand and for metal resistance in Roodepoort. The findings suggest that localised pollution profiles are associated with unique microbial community structures and genetic potentials, providing a genomic basis for proposing site-specific bioremediation strategies. The research underscores the necessity for measures that take into account pollutant composition, soil pH, and microbial adaptation.

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Discoveries in Agriculture and Food Sciences • 2026

This paper discusses possible factors limiting microbial cell protein (MCP) synthesis in rumen microbial cells including their nutrient transport system, their proteasomal concentration for peptide feed-forward activation (FFA) and the energy supply from ATP/NADPH for proteomic cell functions. There is an oscillating pattern with diurnal feeding like a wave function in microbial numbers and their activities in producing end products from energy fermentation. This paper then discusses whether the peptide are at optimum concentrations with the feeding pattern. It mentions possible factors that impact peptide concentration on protein synthesis. These are the proteases in and from the feed material and microbially, the limits by transport systems into the cell’s milieu and the limits for dietary preformed amino acids (PFAA) that are reached for rumen microbial cells. Rates of microbial cell protein (MCP) synthesis are limited by the half-life of mRNA transcripts, their functional attachment to their ribosomal units, the half-life depending on the transcriptional levels, rates of RNA exohydrolases and proteasomal concentrations and their rate of peptide generation acting via FFA as stipulated by the Protein Energy Theory for MCP synthesis. Manipulation of transcription factors (TF) is proposed here for proteasomal concentrations in the cell using earlier developed technology referred to as peptide nucleic acid (PNA) Vit B12-carriered biologics intracellularly. There is initial evidence showing that when an endoglucanase alone is genetically manipulated in a non-continuous culture system that with fermentation more ATP is produced with lactic acid end product. As proposed, it still has to be ascertained whether the manipulated ATP supply for energy would suffice to maintain cellular growth with the cellulases involved and whether the resulting proteasomal concentrations with their ‘catalytic’ peptides from proteins (damaged or in excess) in the cell would suffice to cause an effect on rumen MCP synthesis.

[object Object], [object Object], [object Object] et al.

ISME Communications • 2026

Abstract Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. While forest-to-agriculture conversion fundamentally reshapes plant-microbe-soil interactions and P cycling, these dynamics are further modulated by the intensity of land management. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus monoculture. We investigated how microbial and low molecular weight organic compounds (LMWC) composition interacted with soil physicochemical attributes, acid phosphatase activity, and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to mineral fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and LMWC composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus monoculture. Pseudomonadota and nutrient-rich LMWC were more abundant in the agroforest, whereas Ascomycota and nutrient-poor LMWC predominated the citrus plantation. Genes related to “P acquisition” were more abundant in forest and agroforest soils, while genes related to “P-compound synthesis” were more abundant in the citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and LMWC resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

Antibiotics remain central to modern poultry production, but their long-term and sometimes poorly managed use has markedly altered gut microbial ecology, effectively transforming the intestine into a substantial reservoir of antibiotic resistance genes (ARGs). In poultry, the composition of ARGs reflects not only resistant bacterial taxa but also the activity of mobile genetic elements, shifts in gut metabolic conditions, and features of the surrounding production system. This review synthesizes current understanding of both the structural and functional features of the poultry resistome, with particular attention to key bacterial hosts and the mobile genetic elements they carry. We further evaluate how different antibiotic-use patterns and additional co-selective pressures alter microbial communities and contribute to the persistence of ARGs. We also delineate the major transmission pathways that link breeder flocks, hatcheries, production facilities, and manure management, and interpret these connections within a One Health perspective. Particular emphasis is placed on microbial and nutritional interventions that influence gut microbial interactions, epithelial barrier integrity, and metabolic signaling. Drawing on these findings, we propose a resistome–microbiome–metabolome axis that links microbial taxa, resistance elements, and key metabolic signals, offering a conceptual framework for developing more targeted antimicrobial resistance mitigation strategies in poultry systems.

[object Object], [object Object], [object Object] et al.

Microorganisms • 2026

Background/Aim: Fermented soybean-based products are known to influence gut microbial composition; however, the long-term effects of multicomponent soybean fermented preparations on gut microbiota and colonic mucosal features remain insufficiently characterized. This study examined the effects of a commercially available soybean fermented preparation (SFP), containing additional fermented plant and marine derived components, on gut microbial community structure and colonic histological features in BALB/c mice. Methods: BALB/c mice received oral SFP (1000 mg/kg) for 30 and 60 days. Gut microbial communities were analyzed using full-length rRNA operon sequencing. Colonic mucosal architecture and goblet cell density were evaluated via histological analysis (H E). Results: SFP supplementation induced significant β-diversity separation at both 30 and 60 days (p 0.05), indicating consistent restructuring of the gut microbial community. While alpha diversity (Observed OTUs) remained stable at 30 days, Shannon and Simpson indices were significantly reduced at 60 days (p = 0.001), indicating reduced community evenness driven by increased dominance of specific taxa, including Duncaniella. At the genus level, SFP administration was associated with increased relative abundances of Akkermansia, Lactobacillus, and Duncaniella, accompanied by reductions in several genera previously linked to dysbiosis. Histological analysis demonstrated a significant increase in goblet cell density (p 0.01) in SFP-treated mice. Conclusions: Long-term SFP supplementation was associated with sustained alterations in gut microbial composition and measurable histological changes in the colonic mucosa. While these findings indicate that SFP intake influences microbial structure and goblet cell abundance, further studies are required to determine the functional and physiological implications of these changes, particularly in relation to epithelial barrier function and host health.

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bioRxiv (Cold Spring Harbor Laboratory) • 2026

Microbial ecological dynamics in temporally varying environments are often mediated by the physiological responses of community members. Linking physiological responses to ecological dynamics remains challenging and ultimately limits our ability to understand the response of microbial communities to environmental change. Here, we evaluated the physiological response of microorganisms to changing conditions by applying a macroecological approach to a multi-year timeseries of paired ribosomal RNA and DNA measurements from a freshwater microbial community. We found that the dynamics of both microbial RNA and DNA displayed strong seasonal oscillations, with phylogenetically distant species oscillating on similar timescales with varying amplitudes. Despite this variation, several fundamental macroecological patterns displayed the same regularities observed in other biomes, while others clearly deviated due to the sustained oscillations. These deviations motivated the development of a minimal ecological model that accounts for oscillations, with seasonal dynamics captured by a time-dependent carrying capacity. Based on previous studies, we interpreted the ratio of RNA and DNA (RNA:DNA) as a proxy of ribosome concentration and evaluated two physiological hypotheses. First, we tested whether RNA:DNA explained changes in DNA over time within a given community member, finding that the commonly-used ratio had a limited predictive capacity. However, RNA:DNA across community members was predictive of proxies of growth, a result consistent with the interpretation that RNA:DNA reflects growth. By examining environmental variables with similar seasonality, we found that temperature provided a reasonable explanation for dynamics of both RNA and DNA, though not RNA:DNA. The results of this work provide a macroecological understanding of ribosomal RNA barcoding and identify the limitations of RNA:DNA as a measure of microbial physiology.

Environmental research • 2025

Green electrosynthesis of hydrogen peroxide (H 2 O 2 ) is a research hotspot in environmental chemistry, particularly for wastewater and sanitation applications, with microbial fuel cells (MFCs) offering a self-sustaining route for in situ production. This investigation showcases the application of chemically activated bagasse biochar (AcBC), a graphene-like carbon material, as a cathode catalyst in a ceramic membrane-fitted MFC for H 2 O 2 generation and bisphenol A (BPA) degradation. The AcBC had an exceptionally high specific surface area of 1604 m 2 /g and mimicked the physicochemical characteristic of graphene. The MFC having the AcBC-catalysed cathode attained a maximum H 2 O 2 yield of 248. 9 ± 12.5 mg/L (retention time of 12 h) and peak power density of 125.62 ± 5.62 mW/m 2 . Moreover, this system was tailored into a bioelectro-Fenton system by doping Zn-Fe over AcBC (Zn-Fe/AcBC) that instigated hydroxyl radical formation, thus responsible for removing 95.46 ± 3.50 % of Bisphenol A (BPA, initial concentration = 10 mg/L) in 300 min. Total organic carbon (initial concentration = 47.1 ± 2.3 mg/L) of BPA-containing real wastewater was reduced by 51.4 ± 3.6 % in 300 min while consistently achieving >90 % removal of BPA over eight continuous cycles. Thus, this research demonstrates the potential of biomass-derived graphene-like carbon in catalyzing green H 2 O 2 synthesis for removal of biorefractory organics while achieving sustainable wastewater treatment.

Bioresource technology • 2025

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

Bioresource technology • 2025

Microbial electrosynthesis (MES) utilizes electrical current to convert CO 2 into various products via electroactive microbial activity at the cathode. Methane production in MES relies on methanogens within the cathode biofilm and is influenced by various factors including the type of ion exchange membrane, which plays a critical role but remains underexplored, particularly regarding ion transport mechanisms. This study examined methane production in MES reactors equipped with cation exchange membranes (CEM-MES) and anion exchange membranes (AEM-MES) at cathodic potentials of -1.0 to -1.2 V (vs. Ag/AgCl). AEM-MES produced 10.1 times more methane than CEM-MES. Despite elevated catholyte pH and greater pH imbalances in AEM-MES, methane production was primarily governed by H 2 production rate rather than pH imbalance. The microbial community of cathode biofilm was significantly influenced by membrane type, with Methanobacterium prevailing in AEM-MES, correlating with reactor performance. AEM-MES demonstrated enhanced methane production, particularly at cathodic potentials that minimized hydrogen evolution.

Bioelectrochemistry (Amsterdam, Netherlands) • 2025

Due to its metabolic versatility, mixed communities of purple phototrophic bacteria could be exploited for production of added value products using an electrode as electron donor. Indeed, microbial electrosynthesis has already been proved as a suitable strategy for polyhydroxybutyrate production under photoautotrophic conditions. In contrast with classical biofilm-based electromicrobiology studies, fluid-like electrodes can tune planktonic microbial metabolism to enhance biodegradation rates in brewery wastewater. In this work we have explored polyhydroxybutyrate production in a mixed community enriched from brewery wastewater using a photo-microbial electrochemical moving bed reactor (photoME-MBR). The bioelectrochemical reactor was operated under cathodic conditions (-0.8 V vs Ag/AgCl) with acetate as carbon source as a mean to evaluate i) PHB production and ii) bioelectrochemical performance. We observed how a cathodic polarization of the moving electrode played a key role on PHB production stimulating both direct microbial electron uptake from the conductive bed and electrochemically produced hydrogen in the vicinity of the current collector. Overall, the polarized reactor outperformed the non-polarized reactor by four-fold regarding PHB production rate. In addition, microbial communities analysis revealed Rhodopseudomonas sp. and Bradyrhizobium sp. as main genera in combination with other electroactive genera like Geosporobacter sp. This work revealed that cathodic moving beds could present a feasible platform for biorefineries and added value products production.

Biotechnology notes (Amsterdam, Netherlands) • 2025

Integrating electrochemistry and biology, microbial electrosynthesis (MES) enhances feedstock-to-product conversion by utilizing electroactive microorganisms to harness electrical energy for driving metabolic pathways. Advances in synthetic biology have improved microbial extracellular electron transfer and increased metabolic pathway efficiency, enabling optimized redox balance, expanded substrate versatility and enhanced bioproduction. Given the growing interest in sustainable chemical production and decarbonization, this mini-review highlights recent progress in MES enabled by synthetic biology, with a focus on engineering efficient microbial cell factories for electricity-mediated bioproduction through waste-derived feedstock utilization and carbon capture. We also highlight key challenges limiting MES scalability and propose future directions to enable industrial-scale deployment, unlocking its potential for sustainable, carbon-neutral production and driving transformative advances in biotechnology.

Bioresource technology • 2025

Electro-fermentation assisted chain elongation (EF_CE) effectively converts organic waste into medium-chain fatty acids (MCFAs), yet the regulatory mechanisms involving multiple electron donors (EDs) require elucidation. This study systematically explored the synergistic effects of ethanol and lactate as EDs on MCFA biosynthesis in EF_CE systems. The cross-niche microbial associations shaped by multiple EDs coupled with inoculation with caproate-synthesizing bacteria led to a 2.9-3.9-fold increase in caproate synthesis. Metagenomic analysis revealed that multiple EDs decreased the relative abundances of genes encoding Mut in the acrylate pathway, while increasing the relative abundances of genes encoding ascB in the Wood-Ljungdahl pathway, and ADH, kor and cdhA in ethanol and lactate oxidation pathways. These findings highlight the dual role of EDs synergy in directing MCFAs production and reshaping microbial networks, offering insights for improving organic waste/wastewater recycling.

Frontiers in bioengineering and biotechnology • 2025

The persistence of fossil fuel-based plastics poses significant environmental challenges, prompting increased research into biodegradable polyhydroxyalkanoate (PHA) polymers derived from cost-effective and sustainable resources. Different microorganisms can produce PHA amongst carbon dioxide (CO 2 )-assimilating autotrophic organisms, particularly noteworthy in carbon capture and utilization (CCU). Autotrophic bacteria have evolved to utilize either light (photoautotrophy) or inorganic chemicals (chemolithoautotrophy) to capture CO 2 , which powers their primary and secondary metabolic activities. This review explores the diversity of PHA-producing autotrophs, the metabolic pathways implicated in autotrophic PHA accumulation, and recent progress in photoautotrophs and chemolithoautotrophs regarding PHA synthesis using CO 2 . Additionally, microbial electrosynthesis for converting CO 2 to PHA is also discussed. Genetic engineering strategies are also emphasized for the autotrophic synthesis of PHA. This review also addresses the challenges and prospects for sustainable PHA production using CO 2 .

Environmental science & technology • 2025

Efficient hydrogen utilization by microorganisms is crucial for improving the energy-to-chemical efficiency in microbial electrosynthesis (MES). We therefore developed a new rectangular zero-gap cell design featuring an extended flow path to improve hydrogen retention and conversion to biomethane. Multiphase flow modeling within porous carbon felt cathodes revealed the new configuration with a trapezoidal inlet substantially reduced flow dead zones and tripled hydrogen retention time versus circular cells. At -1 V vs Ag/AgCl, increasing catholyte flow rate from 0.8 to 2.5 mL/min raised current densities from 19 to 24 A/m 2 (30 °C), reaching a peak Coulombic efficiency (CE) of 82% for methane production (7.0 L/L-d). Further increasing the flow rate to 7.5 mL/min or temperature to 37 °C slightly improved methane production (7.2-7.7 L/L-d) but reduced hydrogen retention in cells based on modeling results, lowering CEs and energy efficiencies due to unreacted hydrogen. Matching cathode potential to flow rates and temperatures could balance H 2 production and retention, significantly improving CE to 96% toward 7.5 L/L-d methane production with a high energy efficiency of 36% (-0.95 V vs Ag/AgCl, 37 °C). These findings underscore the importance of improving flow distribution and hydrogen retention within zero-gap MES cells to enhance energy and Coulombic efficiencies.