Orchards have long faced severe soil erosion, acidification of red soils, low nutrient-use efficiency, and frequent soil-borne diseases. Conventional clean tillage combined with intensive chemical inputs often fails to simultaneously improve fruit yield and quality while safeguarding orchard ecological security. Cover cropping (i.e., managed groundcover vegetation) introduces persistent surface plant cover and introduces continuous inputs of root exudates, litter, and residues, while simultaneously modifying soil moisture, temperature, aggregation, porosity, and nutrient availability. Consequently, it reorganizes the soil microbiome from the rhizosphere scale to community-network scales and drives key ecological processes such as carbon sequestration, nitrogen and phosphorus turnover, and disease suppression. Mechanistically, cover crops (i) enhance the supply of labile carbon through root exudation and residue return, stimulating microbial assimilation and enzyme-mediated decomposition and promoting SOC stabilization via microbial necromass formation-mineral association/aggregate protection; and (ii) optimize microbial habitats by improving aggregate architecture, pore structure, and water-holding capacity, and by regulating pH and nutrient availability, thereby increasing the abundance and functional potential of key guilds (e.g., diazotrophs, nitrifiers/denitrifiers, and microorganisms involved in organic-P mineralization) and their functional gene repertoires. In addition, cover cropping may strengthen system stability and suppressiveness through multi-trophic interactions and reconstruction of the soil micro-food web. However, under drought conditions or during the juvenile-tree stage, trade-offs can emerge due to context-dependent tree-groundcover competition for water and nutrients. Future progress requires long-term field experiments integrating multi-omics, isotope tracing, and process-based flux measurements to establish causal evidence chains and scenario-specific models linking management-microbial mechanisms-ecosystem services. Developing operational microbiome-based indicators will provide a scientific basis for groundcover species selection, cover pattern optimization, and fertilizer reduction with improved efficiency, as well as disease mitigation and fruit-quality enhancement.
Lake sediments can act as reservoirs for contaminants and host microbial communities with potential roles in natural ecosystem functioning. This study explored the occurrence of hydrocarbon-degrading bacteria, including "silent" hydrocarbon-responsive populations detectable after selective enrichment, in interfacial sediments of Lake Faro, a brackish meromictic basin in Messina, Italy. Sediment samples collected from five stations were chemically characterized and incubated in microcosms enriched with tetradecane, phenanthrene, or crude oil as the sole carbon and energy source. Chemical analyses revealed that hydrocarbons HCs > 12 were below the quantification limit at all stations, while PAHs were detectable at low concentrations. After 80 days of enrichment, microbial abundance increased, especially in tetradecane and crude oil-amended microcosms, and hydrocarbon-degrading bacteria were selectively enriched. Overall, 25 bacterial isolates were obtained, of which 16 were identified by 16S rRNA gene sequencing and assigned to taxa with reported hydrocarbon-degrading potential, including Isoalcanivorax pacificus, Marinobacter hydrocarbonoclasticus, Pseudoalteromonas sp., Vibirio alginolyticus, and Stappia indica. Several strains showed emulsifying activity, with E24 values up to 60%. These findings suggest that Lake Faro sediments host a latent hydrocarbon-responsive bacterial fraction, with intrinsic bioremediation potential and ecological relevance for natural attenuation processes in transitional aquatic ecosystems.
The symbiotic system of microalgae and fungal microorganisms, such as filamentous fungi, yeasts, and lichen-forming fungi, holds great potential in the fields of environmental remediation and bioresource development. Yet, it faces bottlenecks, including unclear symbiotic mechanisms, high energy consumption for biomass harvesting, poor adaptability to complex wastewater, and insufficient system integration. In this review, we systematically summarized the research progress on microalgae-fungi symbiotic systems in terms of germplasm resource exploration, multifaceted interaction mechanisms, and engineering applications. In particular, we focused on the core advantages of fungal pellet-assisted bioflocculation technology in overcoming the energy bottleneck of biomass harvesting, as well as its optimization strategies. The comprehensive performance of this system in wastewater purification, bioenergy accumulation, and high-value metabolite production was also evaluated. By integrating fundamental mechanisms with engineering application outcomes, we aimed to provide theoretical support and technical guidance for the construction of efficient, stable, and sustainable microalgae-fungi biorefinery platforms. Furthermore, we seek to facilitate the translation of this technology from laboratory research to industrial application.
Yogurt, a fermented dairy food, has been increasingly recognized for its potential to modulate gut microbiota and promote host health. Accumulating evidence suggests that yogurt consumption influences gut microbial composition, diversity, and functional activity. In this narrative review, we synthesized the findings on yogurt-related effects on the gut microbiota, intestinal barrier, microbial metabolites, immune responses, and selected extra-intestinal outcomes. We distinguished traditional yogurt, probiotic yogurt, synbiotic yogurt, fortified yogurt, and non-dairy or regional yogurt-like fermented products, and then organized proposed mechanisms into a hierarchical framework that separated direct yogurt-derived inputs, including starter cultures, added probiotic strains, fermentation-derived compounds, and dairy matrix components, from resident microbiota-mediated secondary metabolites and host downstream responses. Importantly, limitations and controversies, such as variability in yogurt formulations, strain-specific effects, and inter-individual responses, were critically evaluated. Finally, we highlighted future research directions that emphasize standardized study designs, defined endpoints, long-term randomized controlled trials, and integrative multi-omics approaches to support the development of personalized dietary strategies. Together, this review provides a structured framework for understanding the complex interactions between yogurt, gut microbiota, and host physiology, while outlining key steps needed to translate evidence into actionable nutritional recommendations.
In industrial practice, different food-grade materials could be subjected to contamination by microorganisms that are responsible for the spoilage of foods. The chemical sanitizers used to inactivate microbes on the food-grade surfaces have proved effective on vegetative cells, but may not be successful on biofilms, thus encouraging food companies to search alternative ways to eradicate these microbes. For this reason, in this work, two commercially available chemicals based on quaternary ammonium salts (QAC) and alcohols were tested alone or in combination with an enzymatic product against seven-day-old biofilms of three Listeria monocytogenes strains on stainless steel (SS) or poly-tetra-fluoro-ethylene (PTFE). When the sanitizers were applied without any pretreatment, with the QAC, no survivors were detected after 10 minutes at a concentration of 0.75-1.0% on SS; on PTFE, it was necessary to increase the concentration to 1.0% to obtain a total inactivation of the sessile cells for all the tested strains. The use of the alcoholic product enabled us to obtain total inactivation of the sessile cells at a concentration of 50% for contact times greater than 2.5-5 minutes on SS; on the contrary, on PTFE, it was necessary to use the undiluted sanitizer for 10 minutes for all the tested strains. When the enzymatic solution was used as a pre-treatment, the achieved logarithmic reductions were significantly higher than the ones obtained when using the sanitizing products alone: In half of the cases, this combination enabled us to obtain a total inactivation on the biofilm-forming cells.
Taraxacum officinale, a widely invasive plant species in New Zealand, thrives across environments, yet little is known about the seed endophytic microbial communities contributing to its adaptability. In this study, we characterized the bacterial community within T. officinale seeds across an elevation gradient of 10 to 720 meters above sea level. Using PCR-DGGE fingerprinting and 16S rRNA gene sequencing, we characterized bacterial community structures and assessed variations across sites. Bacterial richness declined significantly with increasing elevation, accompanied by distinct shifts in community composition. Non-metric multidimensional scaling revealed clear clustering of communities according to elevation, with higher elevation sites exhibiting more similar and less diverse microbiomes compared to lower elevation locations. A total of six dominant bacterial genera were identified: Pseudomonas, Streptomyces, Clavibacter, Xanthomonas, Stenotrophomonas, and Erwinia. These included core genera detected across sites and location-specific genera associated with particular elevations. These results suggested that elevation acts as an environmental filter shaping seed microbiome assembly, with potential implications for microbial transmission and plant adaptation. The functional consequences of these shifts for plant performance, adaptation, and invasion success remain unknown and require further investigation.
Fungi in the genus Cladosporium (Dothideomycetes, Cladosporiaceae) are widespread in every kind of natural and anthropic terrestrial habitats, where they are reported to be involved in ecological interactions. The developments in marine mycology have demonstrated that, rather than being typically terrestrial, they are also common in the sea. In this manuscript, we examined the synthetic potential of Cladosporium strains recovered from marine organisms and the available information concerning bioactivities of their secondary metabolites. As many as 106 compounds have been identified as products of these fungi so far, belonging to several classes of natural compounds, such as benzopyrones, diketopiperazines, flavonoids, lactones, macrolides, naphthalenones, pyrones, steroids, tetramic acids, and xanthones; 29 of them were first identified from this biological material, representing a valuable source of chemodiversity, which deserves to be investigated in-depth for the related biological properties in view of possible biotechnological exploitation.
Soil salinization is a major constraint on global agricultural productivity, and the application of plant growth‑promoting rhizobacteria offers an important solution for the management and utilization of saline-alkali land. In this study, we aimed to isolate and characterize beneficial rhizobacteria from the halophyte Salicornia europaea growing in coastal saline‑alkali soils, and to evaluate their potential in promoting plant growth under stressful conditions. Among 57 purified bacterial isolates, 3 acetoin‑producing strains, identified as Bacillus sp. HPZ‑9, HPZ‑47, and HPZ‑50, were selected. They produced acetoin at concentrations of 2.30 g·L-1, 2.73 g·L-1, and 2.77 g·L-1, respectively. All strains exhibited broad environmental adaptability, sustaining growth and acetoin production across a pH range of 5-11, NaCl concentrations of 0.3-1.2 mol·L-1, and under moderate drought stress simulated with 20% polyethylene glycol 6000. Notably, HPZ‑9 tolerated NaCl levels up to 2.4 mol·L-1. In pot experiments with maize seedlings, inoculation with these strains significantly increased plant height, stem diameter, leaf length, and fresh and dry biomass of shoots and roots compared to the uninoculated controls (p < 0.05). The most notable improvement was observed in dry biomass, which increased by 49% to 60%. In conclusion, the selected Bacillus strains show strong plant growth‑promoting traits and high tolerance to saline‑alkaline stress. These findings highlight their potential as effective microbial inoculants for promoting crop health and improving saline-alkali soils.
Antagonistic microorganisms from extreme environments have gained great attention from scientists due to increasing threat of global antimicrobial resistance. In this context, previously isolated cold-adapted isolate from Passu glacier Alcaligenes pakistanensis LTP10 was used to extract their antimicrobial metabolites with organic solvents. MIC and MBC assays of the extract were performed. The synergistic effect of LTP10 ethyl acetate extract was studied with known antibiotics against Staphylococcus aureus and Escherichia coli. The extract was analyzed by FTIR, GC-MS, and in silico studies. Ethyl acetate extract of LTP10 has shown a maximum activity of 20 ± 1.0 and 19.3 ± 1.2 mm against Staphylococcus epidermidis and S. aureus, respectively. MIC of the extract was 0.4 and 1.6 mg/mL against S. aureus and E. coli, respectively. FTIR analysis revealed the presesnce of functional groups belonging to alcohols, aliphatic hydrocarbons, and nitrogen containing organic compouns. GC-MS analysis confirmed the presence of important antimicrobial compounds Dodecanoic acid, 3-hydroxy-, 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione, and Pyrimidine-2,4(1H,3H)-dione in ethyl acetate extract of LTP10. A molecular docking study of these compounds has shown that 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione has strong binding affinity of -7.8 kcal/mol against dihydrofolate reductase. Moreover, an ADMET study of the compounds has predicted their good intestinal absorption and non-toxic nature. In this work, we uniquely identify and characterize antimicrobial metabolites of glacier-derived Alcaligenes, combining GC-MS profiling with in-silico analysis. It was concluded that Alcaligenes pakistanensis LTP10 could be considered a good source for antimicrobial compound production, which should be further characterized by analytical techniques.
The present study examined the effects of partially replacing corn silage (CS) with Pleurotus-based spent mushroom substrate (SMS) and oilseeds (OS) on rumen fermentation characteristics, nutrient digestibility, volatile fatty acid (VFA) profiles, and greenhouse gas emissions using a rumen simulation technique (RUSITEC). Four silages were evaluated: A control diet containing 100% CS and three co-ensiled treatments in which CS was partially replaced with Pleurotus-based SMS and OS. The oilseed fraction consisted of equal proportions of soybean and canola seeds. The treatments were: CS90 (90% CS + 5% SMS + 2.5% soybean seed + 2.5% canola seed), CS80 (80% CS + 10% SMS + 5% soybean seed + 5% canola seed), and CS60 (60% CS + 20% SMS + 10% soybean seed + 10% canola seed). Dry matter (DM), organic matter, and crude protein contents were not affected by treatment, whereas ash content increased (P < 0.001) with increasing SMS-OS inclusion. Increasing SMS-OS inclusion significantly reduced non-fiber carbohydrates, hemicellulose and cellulose, while ether extract, neutral detergent fiber, acid detergent fiber, and acid detergent lignin concentrations were increased (P < 0.05). Ruminal fermentation pH, effluent volume, and total gas production showed only numerical differences or trends. DM digestibility increased markedly with SMS-OS inclusion (P < 0.001), rising from 38.7% in the control to 53.0, 49.9, and 52.5% in CS90, CS80, and CS60, respectively, representing improvements of approximately 29-37%. In CS90, organic matter digestibility remained high (P < 0.001) and fiber digestibility was largely the same. Moreover, CS90 had the highest total VFA and acetate, whereas CS60 had the highest propionate proportion (P < 0.05). All SMS-OS diets substantially reduced methane production (P = 0.003) and carbon dioxide emissions (P = 0.014) relative to the control. Methane output declined by approximately 60, 45, and 35% in CS90, CS80, and CS60, respectively (34.2-55.6 vs. 85.7 mg/g DM), while carbon dioxide emissions were reduced by about 49, 26, and 17% (134.7-218.4 vs. 264.0 mg/g DM). In conclusion, co-ensiling corn silage with SMS and oilseeds improved DM utilization while influencing methane production, with reductions observed in all the treatments compared with the control without adversely affecting rumen fermentation stability or fiber digestion under RUSITEC conditions.
Plant-parasitic nematodes are very important plant pathogens that can damage almost all crops worldwide. There has been a progressive decline in the use of chemical compounds because of their high toxicity to humans, livestock, and the environment. Spore-forming Bacilli as excellent biological agents are an effective and eco-friendly solution to control nematodes. However, our previous study showed that genomes of some highly nematicidal strains contain less virulent factor genes. Metabolomics studies based on mass spectrometry (MS) have shown that spore-forming strains can produce five classes of nematicidal secondary metabolites, including macrolide compounds (MCs; selamectin), triazines (Ts; prometon), piprazine derivatives (PDs; diethylcarbamazine), benzene and six-membered heterocyclic compounds (BSMHCs; crotamiton, amodiaquine and diethyltoluamide), and simple aromatic compounds (SACs; phenylacetic acid, benzyl benzoate, and benzyl alcohol). Among the spore-forming species with high nematicidal activity, Cytobacillus firmus synthesizes all five classes of nematicidal metabolites, with a ratio over 30% of PDs, BSMHCs, and SACs. Moreover, B. wiedmannii ZZQ-15, B. mycoides ZZQ-1576, and B. thuringiensis ZZQ-1522, ZZQ-1524, ZZQ-1551, ZZQ-1552, and ZZQ-1553 synthesize novel cyclopeptides with potential nematicidal activity. This study provides a useful method to identify nematicidal metabolites of bacteria.
Probiotics are living microorganisms that improve overall human health by modulating the gut microbiota and enhancing absorption of nutrients and host immunity. Due to the growing demand for probiotics, efforts are being made to search for and characterize new probiotics. Whole genome sequencing has played a significant role in the identification and characterization of many probiotic candidates. In the present study, hybrid assembly (Illumina and Nanopore-based), genomic analyses, and phenotypic evaluations of Lactobacillus rhamnosus 044AE isolated from a dairy sample were carried out to investigate its probiotic potential. The assembled genome of L. rhamnosus 044AE showed maximum homology with L. rhamnosus BIO5326. Downstream analysis of the genome revealed safety, stability, and gut survival features. In the phenotypic assays, L. rhamnosus 044AE exhibited favorable adhesion, aggregation, gut stability (88.96% viability under fasting conditions; 92%-96% viability under fed conditions), antimicrobial, antioxidant, and enzyme activities. Therefore, L. rhamnosus 044AE appears as a potential probiotic candidate for applications in the food, pharmaceutical, and nutraceutical industries.
Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.
Despite the widespread success of combination antiretroviral therapy (cART) in suppressing plasma viremia to undetectable levels, people living with HIV-1 (PLWH) continue to face a significantly elevated risk of chronic inflammation and Serious Non-AIDS Events (SNAEs). In this narrative review, we bridge the critical gap between molecular virology, immunometabolism, and clinical pathology by examining the complex interface of intrinsic immunity and viral persistence. We analyzed the evolutionary "arms race" between conserved host restriction factors, including TRIM5α, APOBEC3G, SAMHD1, BST-2, MX2, and SERINC, and the sophisticated viral evasion mechanisms that facilitate reservoir establishment. We further examined the role of bacterial translocation and gut barrier dysfunction in perpetuating systemic inflammation, emphasizing how HIV-1-mediated depletion of mucosal Th17 cells and disruption of tight junction proteins create a "leaky gut" that permits microbial product translocation despite suppressive therapy. Among viral proteins that may contribute to residual pathology during suppressive cART, we focused on the HIV-1 matrix protein p17, which has been proposed to function as a secreted "viral cytokine" from latent reservoirs, acting through CXCR1/CXCR2 receptors and the RACK1-JAK1-STAT1 pathway. Although primarily characterized in in vitro and ex vivo models, emerging data suggested that p17 may sustain systemic immune activation and metabolic reprogramming; however, its relative contribution compared with other viral proteins (Tat, Nef, gp120) in virologically suppressed patients remains to be fully delineated in human studies. Furthermore, we examined how HIV-1 hijacks cellular bioenergetics by shifting host cells from oxidative phosphorylation to aerobic glycolysis. We present an integrative model that connects restriction factor biology, p17-mediated chronic inflammation, immunometabolic dysregulation, and gut barrier dysfunction into a unified pathogenic framework, distinguishing established mechanisms from working hypotheses. Last, we assessed emerging therapeutic strategies, including CRISPR/Cas9-mediated enhancement of restriction factors, modulation of the mTOR pathway, and novel "Shock and Kill" approaches, stratified by development stage and demonstrated endpoints, offering potential pathways toward a functional cure.
In this review, we summarised the information on probiotic bacteria and their encapsulated forms as functional food components, emphasising survival, technological effects, and product quality. Probiotics from genera such as Bifidobacterium and Lactobacillus are widely used to prevent and manage gastrointestinal and systemic disorders. However, their efficacy is often limited by the loss of viability that occurs during processing, storage, and passage through the gastrointestinal tract. In this article, we analyse the major encapsulation techniques (spray drying, freeze drying, emulsification, extrusion, coacervation, and electrospraying/electrospinning) and emphasise the important function of encapsulating materials, such as proteins, polysaccharides (e.g., alginate, pectin, and chitosan), lipids, and their combinations. Particular focus is given to mixed polymer systems and co-encapsulation with cryo- and protective agents, which can enhance resistance to acid and bile, increase survival by 1-2 log units, and help maintain bioactive compounds. We also consider fermented dairy products, cheese, meat products, and plant-based matrices as carriers for free and encapsulated probiotics. Thus, we show that, when properly selected, these systems can improve microbial stability, modulate proteolysis and lipolysis, and enhance antioxidant and antimicrobial properties without compromising sensory quality. Particular emphasis is placed on emerging plant-based beverages and alternative substrates that could enable probiotics to be consumed by lactose-intolerant and vegetarian populations. Overall, we present encapsulation as a promising strategy for designing next-generation functional foods with predictable probiotic survival and tailored technological and sensory characteristics.
Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.
Radiation enteritis (RE) constitutes a catastrophic collapse of the intestinal holobiont, fundamentally constraining the curative potential of abdominopelvic radiotherapy. Current clinical management, limited by a reductionist focus on host DNA damage, often overlooks the maladaptive ecological feedback loops driving chronic pathology. This review advocates for a definitive transition from empirical probiotic supplementation to microbial synthetic biology for the rational reprogramming of the gut ecosystem. We delineate strategies for thermodynamic engineering, utilizing engineered commensals as living oxygen sinks to scavenge luminal oxygen and nitrate, thereby starving proteobacterial blooms and restoring the physiological hypoxia essential for mucosal recovery. Addressing the Akkermansia paradox, in which nutrient deprivation drives beneficial microbes toward mucin-degrading pathogenicity, we propose genetic domestication (e.g., sulfatase deletion) to decouple immunogenicity from barrier erosion. Furthermore, we explore the design of biological computers equipped with Boolean logic gates to resolve the immunological timing paradox by precisely modulating the cGAS-STING axis and reprogramming macrophage metabolism via the itaconate shunt. Integrating armored polydopamine delivery, genetic entanglement (STALEMATE) for biocontainment, and Gut-on-a-Chip validation, we outline a roadmap for colonic terraformation. This engineering-driven approach aims to actively reconstruct homeostasis, uniquely decoupling epithelial regeneration from tumor protection to improve long-term cancer survival.
Bacterial phytopathogens such as Ralstonia, Xanthomonas, and Pectobacterium pose a serious threat to global food security, while overuse of chemical pesticides has led to resistance and environmental concerns. Trichoderma, traditionally known for antifungal activity, is emerging as a versatile antagonist of bacterial diseases through antibacterial metabolites, immune response, nutrient competition, and rhizosphere modulation. Multi-omics advances have revealed novel biosynthetic gene clusters and host interaction mechanisms, while CRISPR-based genome editing and synthetic biology approaches are enabling the tailored strains with enhanced biocontrol efficiency. Nanotechnology further contributes by facilitating nanoparticle-mediated biosynthesis and controlled-release formulations, improving stability and targeted field delivery. Despite remaining challenges related to field translation, biosafety, and regulation, the integration of omics, genetic engineering, and nanotechnology establishes Trichoderma as a next-generation platform for sustainable and precision crop protection.
