BMC biotechnology • 2025

The present study focused on the antibacterial activity, mechanism and application of Pseudoduganella armeniaca ZMN - 3 extracellular polysaccharide nano silver. Extracellular polysaccharide nano silver was prepared by chemical synthesis and characterized by UV - Vis spectroscopy, Fourier transform infrared spectroscopy, X - ray diffraction, X - ray photoelectron spectroscopy, scanning electron microscopy and transmission electron microscopy. The antibacterial effects of extracellular polysaccharide nano silver on two common pathogens were investigated by agar well diffusion method and broth dilution method. The results showed that extracellular polysaccharide nano silver had significant inhibitory effects on Escherichia coli and Staphylococcus aureus. In addition, by SEM and TEM observation, the conductivity, the leakage of nucleic acids and proteins, the release of reducing sugars, the ATP content, and the alkaline phosphatase level were also measured. The study results indicated that extracellular polysaccharide nano silver could cause the leakage of large biomolecules such as nucleic acids and proteins, reduce the release of sugars, increase ATP content, and lead to the leakage of alkaline phosphatase, ultimately resulting in bacterial death. Finally, the application of extracellular polysaccharide nano silver in antibacterial coating was studied. Antibacterial coating achieved an impressive inhibition rate of 99% against both Escherichia coli and Staphylococcus aureus and could effectively resist bacterial adhesion within 7 days. This study provides a theoretical basis for the potential application of Pseudoduganella armeniaca ZMN - 3 extracellular polysaccharide nano silver in the antibacterial field.

Bioelectrochemistry (Amsterdam, Netherlands) • 2025

Biophotovoltaic (BPV) systems offer a sustainable strategy for solar energy conversion by harvesting the oxygenic photoautotrophic electrons via the extracellular electron transfer (EET) pathway. The photosynthetic pigments absorb light to drive water splitting and generate reducing equivalents for both growth and EET, which thus defines BPV performance is closely tied to light quality. This study evaluated a ferricyanide-mediated BPV system under two light conditions: monochromatic 620-nm red light and broad-spectrum white light, each applied at low (50 μmol photons m -2  s -1 ) and high (300 μmol photons m -2  s -1 ) intensities. Ferricyanide was chosen as the most stable and practical mediator for long-term, outdoor applications. At low intensity, both light types yielded similar photocurrents. However, under high-intensity white light, ferricyanide degraded into toxic cyanide, disrupting cell viability and system function. In contrast, red light preserved mediator stability and significantly enhanced EET, even under very high intensity (up to 1200 μmol photons m -2  s -1 ). While stronger light did not improve cell growth, it boosted EET, emphasizing its role as a potential energy dissipation pathway. These findings highlight the importance of matching light quality to both microbial pigment absorption and mediator stability, and moreover, provide a viable strategy for outdoor BPV deployment.

Bioresource technology • 2025

Biohydrogen synthesis from microalgae represents a promising sustainable energy pathway, attributable to the rapid growth, high photosynthetic efficiency, and carbon dioxide sequestration capabilities of microalgae. This review systematically synthesises and evaluates the principal biological hydrogen production pathways-direct and indirect bio photolysis, photo fermentation, dark fermentation, and microbial electrochemical systems-emphasizing their operational efficiency and recent advancements. Specialised focus is directed towards innovative strategies to augment hydrogen yields, including genetic engineering to elevate hydrogenase expression and refine photosynthetic electron flow, optimisation of culture conditions (light intensity, nutrient limitation, pH), and material-based improvements such as immobilisation and nanoparticle-mediated electron transfer. Genetic alterations have resulted in yield enhancements of up to 60%, whereas optimised cultivation can increase production by 2 to 4 times among microalgal strains. The paper provides an economic analysis of scalability problems and compares the costs of biohydrogen with those of conventional and other renewable hydrogen sources. A SWOT analysis consolidates essential technological strengths, weaknesses, opportunities, and threats, offering a definitive forward-looking framework. This thorough and current synthesis enhances the comprehension of microalgal biohydrogen production and delineates strategic approaches towards feasible, scalable solutions.

Biosensors & bioelectronics • 2025

Monitoring the chlorophyll content of plants can assess crop growth, guide precise fertilization, predict crop yield, etc., which is of great significance for realizing smart agriculture. However, current chlorophyll measurement methods cannot realize this goal. A fast, non-destructive and long-term self-powered chlorophyll monitoring system is proposed. The overall system consists of a miniaturized plant chlorophyll sensing patch (PCSP) and the photovoltaics (PV) -Tribovoltaic nanogenerator for wind energy harvesting (WTVNG)-soil microbial fuel cell (SMFC) triple energy system (PWSS). The PCSP utilizes a reflective optical mode, has a thickness of 4.8 mm and a weight of 2.6 g. It includes a light-emitting diode (LED) and four symmetrical photodetectors (PDs) on a flexible substrate. The whole is wrapped with a light-guiding layer (LGL). The chlorophyll content index (CCI) calculated based on PCSP had a good linear relationship (r 2  > 0.9) with chlorophyll content. PWSS is self-powered by using solar energy as the core power supply and making full use of wind energy in the environment and chemical energy in the soil. The short-circuit current density of the WTVNG at 180 rpm is approximately 7.21A/m 2 . The power density of the SMFC is 1.18 mW/m 3 . Combining the measured chlorophyll content with the LSTM algorithm can be used to categorize stress and predict the chlorophyll content of plants under continuous stress. The overall system is suitable for long-term unmanned monitoring of plants, and detects the stress condition of plants earlier than the traditional chlorophyll meter and visual observation, which have promising applications in smart agriculture.

Chemical reviews • 2025

Semiartificial photosynthesis has witnessed remarkable progress over the past decade, driven by the integration of diverse biological systems with synthetic materials, ushering in the first generation of biohybrid platforms (Biohybrids 1.0). While previous reviews have extensively examined whole-cell biohybrid systems and the fundamental mechanisms underlying solar-to-chemical energy conversion, a critical knowledge gap remains in the rational optimization of their three core components: photosensitizers, microbial partners, and solar energy input. These interdependent elements collectively determine the efficiency, stability, and scalability of biohybrid platforms. To address this gap, this review offers a comprehensive and structured overview of multidisciplinary strategies for the development of next-generation biohybrid platforms (Biohybrids 2.0). It highlights recent advances in photosensitizer design, microbial selection and engineering, energy sources and conversion strategies, interface control and optimization, and state-of-the-art characterization methodologies, while providing a comprehensive summary of a diverse and expanding range of emerging applications. The review also offers a critical appraisal of current limitations and proposes forward-looking research directions that may enable transformative progress toward Biohybrids 3.0. Altogether, this integrative perspective outlines a coherent framework for the rational design of robust, efficient, and application-ready semiartificial photosynthetic systems for real-world and industrial-scale deployment.

Life (Basel, Switzerland) • 2025

Qatar's arid and semi-arid landscapes subject native plants to severe abiotic stresses, including salinity, drought, intense solar radiation, and high temperatures, along with biotic challenges such as herbivory, microbial pathogens, and competition. The ways in which plants coordinate responses to these simultaneous pressures remain insufficiently understood, creating a knowledge gap in desert persistence strategies. This study investigates the integrated defence mechanisms that enable survival under dual stress conditions. We analyse chemical responses such as the synthesis of antimicrobial and phenolic compounds, structural adaptations including thickened cuticles, trichomes, and reinforced cell walls, and physiological trade-offs affecting water-use efficiency and gas exchange. Emphasis is placed on the regulatory role of abscisic acid, which links abiotic stress responses to enhanced pathogen resistance through interconnected biochemical pathways. The study also evaluates the benefits and costs of these structural and biochemical defences. Our findings reveal that native desert species employ adaptive strategies that integrate structural, physiological, and biochemical processes to withstand simultaneous abiotic and biotic pressures. These coordinated mechanisms enhance plant persistence under extreme conditions and play a crucial role in maintaining biodiversity, ecological resilience, and the long-term stability of Qatar's fragile desert ecosystems.

Molecules (Basel, Switzerland) • 2025

Photocatalytic oxidation of microorganisms is a powerful alternative to established disinfection approaches, applicable to a variety of water matrices. Bacterial vegetative cells, spores, fungi, and viruses, represent potential biopathogens and photocatalysis targets. Inactivation efficiency is usually evaluated by assessing viability through culture. However, additional inactivation assessment approaches are needed, as some microbes, despite being unculturable, remain metabolically active and pathogenic. Nucleic acid quantification approaches (qPCR) can assess nucleic acid release and degradation during photocatalysis. We developed a novel multiplex qPCR assay for simultaneous detection/quantification of genomic DNA from different bacterial and fungal species and of MS2 bacteriophage load. Following small-scale solar titanium dioxide photocatalysis on a microbial suspension mixture containing different biopathogen classes, we assessed photocatalytic efficiency by conventional microbiological assays (culture) and our novel molecular assay. Microbiological assays show a significant reduction in microbe viability within one hour of processing, following previously reported patterns of microbial species resistance. Molecular analysis data show that nucleic acids released in solution due to microbial oxidative damage were significantly reduced due to oxidative degradation within six hours. Through targeting different biopathogen classes, our assay could be a useful tool for assessment of photocatalytic microbe inactivation both in laboratory and real-wastewater applications.

ISME communications • 2025

Microorganisms maintain metabolic activity in clouds, with recognized impacts on the chemistry of small organic compounds, radicals, and their precursors. However, how microbial activity is modulated by cloud environmental variables remains unknown. Here we explored the metabolic response of an assemblage of representative microbial isolates from cloud water, composed of a basidiomycetous yeast ( Dioszegia hungarica ) and three bacterial strains ( Rhodococcus enclensis , Pseudomonas syringae , and Pseudomonas graminis ), in synthetic cloud water exposed to contrasted conditions of temperature (5°C vs 17°C), light (dark vs artificial solar light) and oxidants (0 μM vs 250 μM H 2 O 2 ), to mimic typical cloud conditions during winter night and summer day. Metabolomics and metatranscriptomics allowed the identification of 25 differentially abundant metabolites and 218 differentially expressed genes (DEGs). Both summer day metabolomes and metatranscriptomes suggested active mitochondria-driven energy production, with fungal DEGs involved in fatty acids biosynthesis and succinate assimilation, and three differentially abundant acylcarnitines that support fatty acid transport into the mitochondrion for oxidative phosphorylation. In contrast, bacteria displayed DEGs for cell division arrest and components of reactive oxygen species scavenging systems. Under the winter night condition, both bacteria and yeast exhibited a similar prosperous state with DEGs encoding translation, protein repair and turnover, as well as cell cycle related functions. Thus, eukaryotes and prokaryotes may engage in distinct strategies to survive in clouds, depending on environmental conditions. This study consolidates our understanding of microbial roles and interactions in cloud water, paving the way for deeper insights into the chemistry of atmospheric systems.

International journal of biological macromolecules • 2026

Polyhydroxyalkanoates (PHAs) are microbially synthesized polymers that serve as a sustainable alternative to conventional plastics. However, their large-scale production faces challenges due to high production costs. Conventionally, most microorganisms have been reported to produce only PHAs when cultivated under conditions of high carbon content and limited nitrogen and phosphate. In contrast, this study explores the simultaneous production of PHAs and high-value carotenoids by employing halophilic archaea. A pigmented halophilic archaeon Haloarcula argentinensis GUAg231, isolated from the multipond solar saltern of Goa, India, has been studied to co-produce PHAs and carotenoids with 1% glucose as the carbon source. The process resulted in a PHA yield of 2.96 ± 0.12 g/L and a carotenoid yield of 3.75 ± 0.03 mg/L. Fourier-transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) analysis confirmed the PHA produced as poly(3-hydroxybutyrate-co-3-hydroxyvalerate) P(3HB-co-3HV) with a 13.98% hydroxyvalerate (HV) fraction, while the major carotenoid in the halophilic archaeon was identified as bacterioruberin. This dual-production strategy could enhance the economic feasibility of PHA manufacturing, highlighting the potential of halophilic archaea as a viable approach with opportunities for optimization to achieve higher yields of PHA and carotenoids.

International journal of environmental health research • 2025

The Microbial Desalination Cell (MDC) stands out as an innovative and a sustainable technology for both renewable energy generation and water treatment. The choice of electron acceptor significantly influences the efficiency of electricity flow. This study focuses on exploring the MDC performance under different conditions, including variations in cathode electron acceptors, initial pH levels, and hydraulic retention time (HRT). The investigation assesses simultaneous reduction of TDS and power generation from Caspian Sea water, a prominent saline water source in northern Iran, in both open-circuit (OC) and closed-circuit (CC) modes. The findings reveal that sodium hypochlorite, potassium permanganate, and potassium bromate as catholyte achieved TDS reduction rates of 84%, 77%, and 72%, respectively, under CC conditions at pH 5. Furthermore, it was observed that increasing HRT and pH levels lead to a decrease in desalination efficiency and power generation. Notably, the study highlights that the maximum power density was attained using permanganate, hypochlorite, and bromate as catholyte in both OC and CC configurations. By showcasing the adaptability of MDC performance with different cathode electron acceptors under varying conditions, this research offers valuable insights for optimizing MDC efficiency when treating real saline water sources.

Scientific reports • 2025

Microbial desalination cells (MDCs), as an emerging desalination technology, have attracted increasing attention in recent years due to their ability to simultaneously achieve salt removal and wastewater treatment without the need for external energy input. In this study, the performance of two MDC systems with different cathode types-a biocathode (MDC1 # ) and a permanganate cathode (MDC2 # )-was comparatively evaluated for the treatment of saline wastewater, with a particular focus on voltage output, desalination efficiency, and chemical oxygen demand (COD) removal. Experimental results showed that the average output voltage of MDC2 # reached 742.02 mV, which was significantly higher than that of MDC1 # (695.6 mV). Its maximum power density was as high as 6.22 W/m3, approximately six times that of MDC1 # . Moreover, MDC2 # exhibited a higher average chloride removal rate in the desalination chamber (32.34 mg/h), compared to 17.13 mg/h for MDC1 # , indicating superior desalination performance. However, in terms of electron recovery, MDC1 # achieved a much higher average Coulombic efficiency (28.8 ± 18.7%), nearly three times that of MDC2 # , suggesting more efficient electron utilization with the biocathode. Regarding ammonium removal, MDC1 # demonstrated a higher initial removal efficiency within the first 96 h (74.3%, with an average rate of 4.17 mg/h), but this declined sharply over time, with the later-stage rate dropping to only 0.32 mg/h (less than 10% of the initial rate). In contrast, MDC2 # maintained a relatively stable ammonium removal rate throughout the operation (ranging from 0.58 to 3.27 mg/h, with an average of 1.92 mg/h). In addition, both systems achieved stable COD removal at the anode, with efficiencies consistently above 85%. Overall, the permanganate cathode is more suitable for applications that require high voltage output and efficient desalination, whereas the biocathode shows significant advantages in organic pollutant removal and energy recovery. This study provides a theoretical foundation for the rational selection of cathode types based on the characteristics of saline wastewater, offering valuable guidance for optimizing MDC system performance.

Foods (Basel, Switzerland) • 2025

Surface display technology has revolutionized whole-cell biocatalysis by enabling efficient enzyme immobilization on microbial cell surfaces. Compared with traditional enzyme immobilization, this technology has the advantages of high enzyme activity, mild process, simple operation and low cost, which thus has been widely studied and applied in various fields. This review explores the principles, optimization strategies, applications in the food industry, and future prospects. We summarize the membrane and anchor protein structures of common host cells ( Escherichia coli , Bacillus subtilis , and yeast) and discuss cutting-edge optimization approaches, including host strain genetic engineering, rational design of anchor proteins, innovative linker peptide engineering, and precise regulation of signal peptides and promoters, to maximize surface display efficiency. Additionally, we also explore its diverse applications in food processing and manufacturing, additive synthesis, food safety, and other food-related industries (such as animal feed and PET packaging degradation), demonstrating their potential to address key challenges in the food industry. This work bridges fundamental research and industrial applications, offering valuable insights for advancing agricultural and food chemistry.

Environmental pollution (Barking, Essex : 1987) • 2025

Bisphenol A (BPA) analogues are a group of emerging contaminants as substitutes for BPA. Bacteria are acknowledged as indispensable parts of the ecosystem, whereas the bacterial toxicity data for BPA analogues is still lacking. Herein the wild-type and Δacriflavine resistance B (acrB) strains of E. coli K12 were exposed to BPA and bisphenol S-MPE (BPS-MPE), a BPA analogue already detected in environmental compartments but less studied yet, respectively. In comparison with the control, the growth of the wild-type strain was significantly promoted by 50 nmol L -1 BPA and BPS-MPE at stationary phase, while that of the ΔacrB strain increased initially but decreased thereafter at 5 and 50 nmol L -1 BPA and BPS-MPE. Therefore, lack of acrB confers a higher susceptibility to BPA and BPS-MPE. They induced hormetic effects on the expressions of acrB and Type II topoisomerases and a concentration-dependent decrease in the ATP levels. The predicted minimum inhibitory concentrations of BPA and BPS-MPE by Kernel Partial Least Squares dendritic model agree well with the measured values. Transcriptomics showed that BPA and BPS-MPE not only resulted in significant enrichment of Gene ontology terms relevant to transport, ATPase activity, binding and cell membrane, but also inhibited oxidative phosphorylation and ATP binding cassette transporters pathways. Trend analysis revealed the presence of three significant clusters, all of which showed higher changes in gene expression caused by 0.5 nmol L -1 BPS-MPE compared to 0.5 nmol L -1 BPA consistently. Our results unveiled BPA-like toxicity of BPS-MPE to E. coli K12 at environmentally relevant concentrations.

Environmental technology • 2025

Inorganic salts and nitrogen compounds are prevalent in wastewater from chemical, pharmaceutical, and petrochemical industries. Nitrogen-containing wastewater in high-salt environments was treated in an anaerobic fluidised bed microbial fuel cell (AFB-MFC) with carbon brush biofilm anodes and macroporous adsorption resin (MAR) as a multifunctional biofilm carrier. During the experiment, the DO value of the influent was maintained between 0.2-0.5 mg/L, and the nitrogen concentrations in the influent were 0.3, 0.5, and 1.0 g/L, respectively. Materials Studio (MS) software was used to construct nitrogen-containing compounds and MAR models. The simulation result indicated that MAR exhibited the best adsorption performance on nitrite nitrogen, with an adsorption heat of 117.7985 kJ/mol. MAR effectively removes nitrogen-containing compounds through van der Waals forces and hydrogen bonding interactions. The simulation closely matched experimental results, with a high R² (>0.99) indicating strong regression significance. The highest removal efficiency of ammonia nitrogen, nitrite nitrogen, and nitrate nitrogen was 97.97 ± 0.97%, 98.81 ± 1%, and 99 ± 0.47%, respectively. The results showed that the desalination efficiency was 55%, 41.5%, and 27% at salinities of 10, 20, and 30 g/L, respectively. The maximum output voltage and power density achieved using carbon brush as biofilm anodes in the AFB-MFC were 651.34 mV and 174.97 mW/m², respectively. The high-throughput sequencing analysis results revealed a significant relative abundance of the dominant electroactive bacteria present on the carbon brush, such as Proteobacteria , Firmicutes , Bacteroidota , and Chloroflexi , and also identified such superior denitrification bacteria as Citrobacter , Corynebacterium , Pseudomonas , and Castellaniella etc.

Environmental monitoring and assessment • 2025

Algae-based desalination, biosorption, and bioaccumulation of polluted water offer a low-cost, passive-energy alternative with ecological benefits. This review presents a comprehensive analysis of microalgae-based biodesalination for salt removal and environmental remediation. Results suggested that algae operate faster in salt removal for biosorption and remediation and depend on salt tolerance, adaptability with system configurations, water characteristics, harvesting methods, and reuse potential. Biosorption kinetics, zeta potential regulation, and abiotic factors (pH, light, and salinity) are important for optimum algal-dependent wastewater remediation. Strains like Dunaliella salina and Picochlorum exhibited optimum salt remediation potential and lipid accumulation and may emerge as sources of biofuel even under high saline conditions. Algal strains could be used as biosensor platforms with emerging hybrid technologies (nanoparticle-enhanced systems and microbial fuel cells) for efficient environmental monitoring. Integration of algal residue with conventional technologies like reverse osmosis could enhance cost-effectiveness and scalability in the desalination process. Overall, algae-based desalination represents a promising, environmentally sound solution to address reduced wastewater remediation, particularly in remote or resource-limited regions.

Bioresource technology • 2025

Microbial desalination cells (MDCs) have traditionally employed simplified NaCl solutions as feedwater for synchronous desalination and bioenergy recovery. Nevertheless, the specific mechanisms by which MDCs remove complex multi-ions from saline wastewater remain obscure. This study thoroughly investigated ion migration, bioelectrochemical dynamics, and microbial ecological responses across three distinct configurations: monovalent ions - PMDC, divalent cations - CMDC and anions - AMDC. Results showed desalination efficiencies exceeding 97 % among all bioreactors, with CMDC outperforming AMDC yet lower than PMDC. The transmembrane behavior of ions with varying charges was regulated by electric field gradients, with cation migration hierarchies following Na + > Ca 2+ > Mg 2+ and anion transfer prioritizing CO 3 2- > SO 4 2- > Cl - . A mathematical model further elucidated variations in ion diffusion and salt transfer. The CMDC exhibited peak power density (927 mW/m 2 ), achieving 1.57 and 1.99 times that of PMDC and AMDC, due to reduced ohmic resistance and improved cathodic kinetics. Prolonged operation exposed critical limitations: multivalent cations induced 21.4 % desalination efficiency loss and 38.3 % power decline via membrane scaling and biofouling accumulation. Microbial community analysis highlighted Lentimicrobium (26.7 %), Desulfomicrobium (12.3 %), and Oscillochloris (9.2 %) as dominant electroactive genera, with their synergistic interactions and functional metabolic pathways (carbon fixation, nitrogen metabolism, and sulfur reduction) critically enhancing organic degradation and bioelectricity generation in multi-ionic MDCs. This comprehensive study bridges critical gaps in understanding electrochemical and microbial responses in MDCs treating hypersaline wastewater, advancing their practical implementation.

Bioelectrochemistry (Amsterdam, Netherlands) • 2025

This study introduces a new hexagonally structured multi-anode shared cathode microbial desalination cell (MASC-MDC) designed to address the limitations of traditional MDCs in handling hypersaline solutions. The hexagonal shape shortens the intermembrane distance to 2 cm, significantly reducing internal resistance (∼50 Ω) and enhancing bioelectrochemical performance. Compared to a conventional three-chamber MDC, the MASC-MDC achieved better results, including a higher open-circuit voltage (646 vs. 553 mV), faster desalination (95.71 % in five cycles vs. 94.29 % in seven), higher desalination rate (0.27 vs. 0.195 g·L -1 ·h -1 ), and greater maximum power density (162.2 vs. 119.2 mW·m -2 ). The system also attained effective pollutant removal with 90.05 % COD reduction. These findings demonstrate that the multi-anode shared cathode design enhances ion transport, bioenergy production, and wastewater treatment simultaneously, offering a scalable, self-powered alternative to energy-intensive desalination methods.

Environmental pollution (Barking, Essex : 1987) • 2025

The algal biocathode offers a sustainable, cost-effective alternative to chemical cathodes in microbial desalination cells (MDCs). This study evaluated Chroococcus minor as a biocathode with Shewanella putrefaciens MTCC 8104 (Sh-MDC) and mixed culture (Mx-MDC) exoelectrogens in a novel concentrically arranged MDC using sago effluent as anolyte and 30 g/L NaCl in the central desalination chamber. The influence of microalgal growth on MDC performance was monitored over 30 days. Sh-MDC achieved a peak power density of 31.7 ± 0.6 mW/m 2 , while Mx-MDC reached 20.8 ± 0.4 mW/m 2 between days 10-15, comparable to abiotic MDCs. Mx-MDC recorded the highest COD removal (92.9 ± 2 %) between days 25-30, along with significant removal of metals (Al, Ag, Pb) from sago effluent. Microbial community analysis of Mx-MDC revealed a high abundance of electrogenic populations. The system's application for brackish water treatment in the desalination chamber was assessed. To improve performance, plant-derived mediators, Chrysopogon zizanioides (vetiver) and Allium cepa (onion) peel extracts were added to the anode chamber. The C. zizanioides-mediated Mx-MDC exhibited a 1.98-fold increase in power density compared to non-mediated systems. COD removal and desalination efficiencies improved to 94.3 ± 1.9 % and 21.5 ± 0.43 %, respectively. Thus, C. zizanioides extract is a sustainable mediator enhancing the performance of Mx-MDC over Sh-MDC. Optimizing electrogenic populations and adapting Chroococcus minor to brackish conditions can further improve MDC efficiency, while the harvested algal biomass offers potential reuse, supporting a circular economy.

Bioresource technology • 2026

The regulatory role of carbon/nitrogen (C/N) ratios in microbial desalination cells (MDCs) treating ammonium-rich wastewater was investigated, focused on the interplay with salinity gradients and electron transfer. Through integrated analysis of electrochemical behavior, nitrogen pathways, and microbial succession under varying C/N ratios (18, 9, and 6), optimal performance was achieved at a C/N ratio of 9, demonstrating high removal efficiencies for carbon (93.4 %), nitrogen (86.5 %), and salt (90.7 %), alongside peak power density of 586 mW/m 2 . This enhancement was attributed to improved biofilm viability, lower charge transfer resistance, and protein-enriched extracellular polymeric substances that facilitated efficient electron shuttling. Conversely, lower C/N ratio induced ammonium toxicity, significantly increasing resistance and suppressing electroactive bacteria. The enriched genera (Vitreoscilla, Brevefilum, and Smithella) and key functional pathways (nitrification, denitrification, and anammox) synergistically drove bioelectricity enhancement and nitrogen transformation. This work establishes C/N stoichiometry as a master regulator of the electro-microbiological nexus in hypersaline wastewater treatment.

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Wellcome Open Research • 2026

We present a genome assembly from from a specimen of the clarki ecotype of an individual specimen of the lettuce sea slug Elysia crispata (lettuce sea slug; Mollusca; Gastropoda; Plakobranchidae). The genome sequence has a total length of 542.56 megabases. Most of the assembly (87.52%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 14.17 kilobases. Additionally, we sequenced the chloroplast genomes of two dietary algae, Penicillus capitatus and P. lamourouxii , from plastids sequestered inside of slug cells where they remain photosynthetically active. Gene annotation of this assembly by Ensembl identified 18 436 protein-coding genes. From the metagenome data, we recovered six bins, of which four were high-quality MAGs.

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Frontiers in Bioengineering and Biotechnology • 2026

Introduction: Freshwater scarcity represents a major constraint for the sustainable industrial-scale cultivation of microalgae. This study investigates the feasibility of producing Scenedesmus almeriensis using seawater in 3.1 m 3 tubular photobioreactors under winter-spring conditions. The appearance of algal predators represents a significant challenge in industrial facilities, and this research also explores whether seawater can serve as a strategic water source for more resilient and efficient production systems. Methods: Biomass productivity and microbial diversity were compared between freshwater and seawater-based cultures under batch and semi-continuous regimes at dilution rates of 0.1, 0.2, and 0.3 day -1 . The production was carried out in duplicate using identical tubular photobioreactors. Analytical determinations included measuring biomass concentration, chlorophyll fluorescence, and oxygen production via photorespirometry. Microbial diversity was assessed through microscopy and metagenomic analysis (18S and 16S rDNA) to identify taxonomic classifications and potential biotic contaminants. Results and Discussion: Maximum biomass concentrations reached 0.60 and 2.15 g·L -1 in freshwater and seawater, respectively. Production using seawater led to a higher biomass productivity (0.18 g·L -1 ·day -1 ) compared to freshwater (0.06 g·L -1 ·day -1 ) at a fixed dilution rate of 0.1 day -1 . Seawater cultures exhibited greater stability and higher photosynthetic efficiency, with Scenedesmus dominating up to 70% of the microalgal community due to reduced contamination by zooplankton, fungi, and ciliates. In contrast, freshwater cultures were rapidly degraded by rotifers and anaerobic fungi, leading to a culture crash when dilution rates were increased. These findings highlight the potential of seawater to act as a biological barrier against contaminants while significantly reducing freshwater requirements in industrial microalgae production.

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

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Understanding emerging functions at the scale of a bacterial community is a major challenge in microbial ecology and could lead up to promising tools for engineering microbial communities, for example in bioremediation. Here, through a top-down approach we obtained compositional variants of pesticide and antibiotics-degrading communities and further investigated communities features associated with their degradation abilities. We first tested whether diversity index or functional genes abundance could reliably be used as a proxy for this function, and obtained encouraging, albeit variable results. Further, through the use of statistical tools borrowed from the genomic selection literature, we were able to derive accurate prediction of the mineralisation potential of a bacterial community, based on its composition. However, the parallel between genotype-phenotype and community composition-mineralisation potential suffers a crucial caveat: bacterial abundances vary on a much wider scale than allele dosage at a given locus and are prone to change over time (particularly at the mineralisation scale). Here we observed that using presence/absence data instead of relative abundance can overcome these limitations and provide a clearer functional signal for mineralisation prediction through linear regression models. Random forest can also intrinsically deal with microbial data without transformation and select for significant predictors. We suggest drawing inspiration from the tools and concepts used in genotype-phenotype mapping to elucidate microbial functions at the community level while keeping in mind the significant differences between these two fields. This parallel is here exemplified by the concept of microbial architecture of degrading functions, akin to the genetic architecture of phenotypic traits.

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World Journal of Microbiology and Biotechnology • 2026

Abstract The immobilization of plant growth-promoting rhizobacteria (PGPR) in biodegradable polymeric networks is a promising strategy for protecting them from environmental stresses and optimizing their plant-beneficial functions. In this study, a microbial consortium of Pseudomonas stutzeri and Beijerinckia mobilis was immobilized in bacterial cellulose (BC) produced by Komagataeibacter xylinus . Its efficacy was evaluated in onion ( Allium cepa ) under three treatments: uninoculated control, free cells, and immobilized cells, during a field trial conducted in the 2025 winter cropping season at El-Kharga Oasis, New Valley Governorate, Egypt. Both inoculation forms significantly ( P    0.05) enhanced plant growth, nutrient uptake, and soil fertility, with immobilized cells increasing bulb yield by 44.9% over the control and outperforming free cells. Treatments elevated N, P, K levels in bulbs and soil, with immobilized cells showing superior nutrient mobilization. The microbial diversity in the onion rhizosphere was assessed at harvest. Ecological diversity indices revealed that bacterial treatments, especially in immobilized form, were associated with a short-term reduction in overall microbial diversity, reflecting selective enrichment of plant-beneficial taxa while suppressing non-beneficial competitors. This functional shift enhanced rhizosphere efficiency without long-term detriment to soil health, as confirmed by post-harvest observations. The novelty of this work lies in the field-scale validation of BC as a biodegradable, highly porous carrier that protects PGPR under arid conditions while simultaneously modulating rhizosphere communities. This study highlights microbial immobilization in BC as a robust, eco-friendly approach to enhance crop yield and soil nutrient dynamics, offering a scalable strategy for sustainable agriculture. Photo 1 Graphical illustration showing PGPR immobilization in biocellulose and its effect on onion growth and nutrient uptake through microbiome modulation. Graphical abstract

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bioRxiv (Cold Spring Harbor Laboratory) • 2026

Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand life's diversity in the environment.

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

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Adipic acid (1,6-hexanedioic acid) is a key building block for nylon-6,6, a widely used polymer in the global chemical industry. Current industrial production relies on petrochemical feedstocks and nitric acid oxidation of cyclohexane/cyclohexanol mixtures, releasing nitrous oxide, a potent greenhouse gas. Biotechnological routes offer sustainable alternatives but have been limited by low yields or reliance on multi-strain systems. Here we report a one-pot, single-strain microbial process for the efficient conversion of guaiacol - a lignin derived aromatic - into adipic acid. By integrating heterologous Rieske non-heme iron monooxygenases from Cupriavidus necator N-1 with systematic process optimisations in engineered Escherichia coli, we achieve near-quantitative conversion with 97% yield and titres of 1.5 g/L in aqueous, lab-scale reactions. This work demonstrates a novel and efficient strategy for lignin valorisation through engineered microbial synthesis, providing a new sustainable and scalable route to adipic acid.

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

Frontiers in Microbiomes • 2026

Background Whether domestication, post-domestication spread, and breeding affected the maize leaf endosphere microbiota is poorly understood despite the well-known effects of those processes on the crop’s genetics and responses to the environment. We examined the leaf endosphere microbial communities associated with three plant groups (Zea mays): teosintes, maize landraces, and maize elite inbreds. The teosintes group included Balsas (Z. mays parviglumis) and perennial (Zea diploperennis) teosinte, and each maize (Z. mays mays) group included genotypes from Mexico and USA. We used 16S-V4 region amplicon sequencing of the leaf endophytic microbiota to infer how the microbial communities of inbred maize may have been shaped by the crop’s evolution, and whether they were affected by: (i) the transition from a perennial life history to an annual life history in the teosintes; (ii) domestication of maize from Balsas teosinte; (iii) northward spread of landrace maize from Mexico to the US; and (iii) breeding of landrace maizes to produce elite inbreds. Results The leaf endophytic microbial community differed among the plant groups and genotypes, and was affected by domestication, as indicated by a decline in bacterial diversity and changes in microbial community structure between wild (teosinte) and domesticated (maize) Zea. While the microbial community structure was stringent and regulated in the teosintes, it was variable in the maize landraces and inbreds, as evidenced by greater distances to centroid based on Euclidean dissimilarity metric. This pattern was suggestive of microbial dysbiosis in the leaf endosphere associated with domestication and is consistent with predictions of the Anna Karenina principle. This finding marks the first evidence of dysbiosis associated with domestication. FAPROTAX predictions suggested that the teosintes may harbor microbial communities enriched in taxa associated with cellulolytic, chitinolytic, and nitrate respiration functions, while the maizes showed higher fermentation and nitrate reduction functions. Conclusions Our results showed that the leaf endosphere microbial community structures in maize are consistent with alterations associated with dysbiosis. Our findings enhanced our understanding of the effects of anthropogenic processes including crop domestication, spread, and breeding on the leaf endosphere of elite maize cultivars, and may guide the development of evolutionarily-and ecologically sustainable biofertilizers and biocontrol agents.

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

Frontiers in Microbiology • 2026

Background Deep marine cold seeps occurring along the seabed of continental margins are identified by their oasis-like ecosystems, which are largely fueled by the chemical energy of the venting fluids. Seep site 2A-1, situated at ~2,500 m water depth on the Scotian Slope of the North Atlantic was discovered in 2021. The seep hosts a large mussel encrusted, carbonate mound with biogenic methane bubbling up from a single vent. The emitted biogenic methane is primarily sourced from ~1 km below the seafloor within the basin bedrock that resides directly above the crest of an underlying salt diapir. Methods A 600-m long transect composed of six push cores was collected across the seep structure. Downcore porewater ions and lipidomic profiles of 24 predominantly archaeal in origin lipid classes were tentatively identified and quantified across the transect. Results The resolved lipidomes comprised of intact polar lipids, core lipids, core lipid degradation products, and photosynthetic pigments. These data were compiled as two-dimensional heatmaps to spatially examine vertical and lateral changes in the subsurface geochemical and microbiological architecture of the seep. Microbially mediated metabolic zones of elevated heterotrophy, denitrification, microbial sulfate reduction, and anaerobic methane oxidation were then mapped across the seep structure based on an integrated analysis of porewater geochemistry, bulk organic matter and its carbon isotope compositions, lipidomic diversity and biomarker proxy patterns. Discussion Increased lipidomic diversity is shown to exist within the seep particularly at boundaries of high lateral geochemical gradients. Biomarker lipid proxies and porewater gradient changes indicate a microbial community dominated by ANME-1 and -2/−3 archaea that is mixed with, but also surrounded by, an envelope of microbial sulfate reduction. Discussion Spatial changes in the stratified system highlight the complex interplay of micro- and macro-seepage and provide insights into the seep’s evolution and impact on microbial dynamics across the carbonate structure.

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

Microbiology Spectrum • 2026

ABSTRACT Microorganisms colonize every external and internal surface of plants, including fruits. Relatively little is known about the fruit microbiome and its role in disease resistance and fruit quality during fruit development and storage. The fruit tissue, the carposphere, is a carbohydrate-rich habitat. Amplicon sequencing of fungal and bacterial communities identified distinct microbial community composition and diversity across tissue types such as the exocarp and mesocarp. We determined microbial richness was highest during bloom and in mature fruits. Endophytic microbes were shared across many fruit development stages, while epiphytic microbes were transient. However, we identified a pattern of succession with increasing diversity of the epiphytic microbiota across the growing season. Notably, we also show that fungal and bacterial taxa with carbohydrate-degrading potential have different abundance patterns across apple developmental stages, which could indicate that host plants have distinct regulation for microbial subgroups or that microbes interact with different elements of host regulatory mechanisms. The identification of a stable microbiota associated with tree fruit, and understanding how those microbes establish and function, will provide fundamental insights regarding the engineering of a consortium of microbes that could thrive under storage and possibly reduce food waste. IMPORTANCE Plant-associated microbes are not well-characterized in specialty crop systems. We describe the fungal and bacterial microbial communities colonizing the surface and interior of apple flowers and fruits over the course of one growing season. This work provides a foundational understanding of microbes present, how the populations change over time, and provides insight into the origins of endophytic microbes. These findings will be used in future apple disease-related research, particularly on the development of organic or biologically based pesticides.

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

Frontiers in Microbiology • 2026

Keratinous waste, a major by-product of agriculture and animal husbandry, is produced in massive quantities and is notoriously recalcitrant to degradation. With the expansion of the poultry and livestock industries, keratinous waste accumulation (e.g., feathers, hooves, and horns) has become a pressing environmental concern. Keratin’s highly cross-linked disulfide bond structure is resistant to breakdown by common proteases. Keratinase, a specialized protease capable of specifically degrading keratin, has emerges as a pivotal tool for the valorization of keratinous waste, demonstrating significant potential in waste management and resource recovery. This review systematically summarizes the enzymatic properties, mechanisms of action, and microbial sources of keratinases. It elaborates on innovative keratinase applications in waste valorization (including biogas production, the generation of bioactive peptides and amino acid feedstocks, and bioplastic manufacturing) and green industries (including leather and textile processing), as well as in the pharmaceutical, cosmetic, and detergent sectors. This review provides an in-depth discussion of the major challenges hindering industrial-scale keratinase application, including low heterologous expression efficiency and insufficient stability under industrial conditions. Finally, it outlines future research directions, encompassing protein engineering, artificial intelligence (AI)-assisted design, and multi-enzyme synergistic catalysis systems, aiming to offer forward-looking theoretical insights for advanced keratinase development and industrial application.

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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.

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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.

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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.