Appl. Microbiol., Volume 6, Issue 3 (March 2026) – 13 articles

Fungal endophytes are microorganisms that inhabit plant tissues without causing disease and emerge as critical mediators of plant stress tolerance, nutrient acquisition, and ecosystem resilience under diverse climate change scenarios. Their unique position within the host allows them to modulate physiological responses more closely than external microbiota. This review explores how endophytic fungi contribute to plant adaptation under climate-induced stresses such as heat, salinity, drought, pollution, and nutrient limitation, with a focus on molecular crosstalk, functional trait modules, and metabolic trade-offs. Key findings emphasize multilayered signaling systems, including MAMP/DAMP recognition, phytohormone regulation, immune tuning, ROS dynamics, and effector deployment, while emerging mechanisms such as cross-kingdom RNA and extracellular vesicle (EV)-mediated exchange are discussed as promising but currently limited in empirical validation within many endophytic systems. Endophytes also enhance nutrient exchange through conditional carbon-for-benefit trade and may shape rhizosphere microbiota and soil activities through plant-mediated inputs. Integrative multi-omics approaches provide predominantly correlational insights into the mechanistic basis of these effects, linking molecular function to ecosystem and community outcomes. These insights have potential applications in climate-resilient agriculture, phytoremediation, and ecosystem restoration; however, their large-scale implementation requires further field-based validation and context-specific assessment. Future priorities should focus on trait-based selection, ecological modeling, and biosafety evaluation to translate microbial functions into reliable field-level strategies that support sustainable crop performance under accelerating environmental stress. Full article

Neopestalotiopsis rosae is an emerging fungal pathogen that causes leaf blight and fruit rot on strawberry. Due to limited fungicide availability and the small number of substances confirmed to be effective against this pathogen, alternative disease control strategies have become a focus of current research. This study aimed to assess, quantify, and compare the efficacy of extracts and inocula of Trichoderma spp. with the conventional fungicide Switch in controlling N. rosae. In the presence of T. harzianum T16 and T. asperellum T23 extracts, conidia production of N. rosae was reduced by 45.0% and 62.7%, respectively. Extracts of T. koningiopsis T10 strongly inhibited both mycelial growth and conidia production (>92.0%), demonstrating efficacy comparable to that of the reference fungicide. Furthermore, T. koningiopsis T10 extracts were able to inhibit N. rosae conidia viability by 55.6%. Under greenhouse conditions, strawberry plants treated with extracts from T. koningiopsis T10 showed protection from N. rosae leaf spots at levels similar to Switch. These findings highlight T. koningiopsis T10 extracts as a promising alternative to chemical fungicides in the integrated management of N. rosae on strawberry. Full article

Celiac disease (CD) is an autoimmune disorder triggered by immunogenic gluten peptides that resist gastrointestinal digestion. The only current treatment is a strict gluten-free diet, which is challenging to maintain. Lactic acid bacteria (LAB) with specific proteolytic systems offer a promising strategy for gluten hydrolysis and potential reduction of immunogenicity. This study aims to isolate and characterize gluten-degrading LAB from traditional Spanish and Algerian dairy products. A total of 27 artisanal dairy samples were collected. LAB were isolated on MRS and Elliker agar. Gluten-degrading activity was screened using a well diffusion assay with cell-free supernatants and a spot assay with live cultures. Active isolates were identified by 16S rRNA gene sequencing. Out of 123 isolates, 40 (32.5%) were positive in the well assay, while 67 (54.5%) were positive in the spot assay, indicating the latter’s higher sensitivity for detecting cell-associated proteases. Halo diameters ranged from 6 to 16 mm. Algerian isolates exhibited significantly stronger activity (mean halo: 12.6 ± 2.1 mm) compared to Spanish isolates (10.2 ± 2.0 mm; p < 0.001). Molecular identification of the 32 most active isolates revealed the following dominant species: Lactiplantibacillus plantarum, L. pentosus, Levilactobacillus brevis, and Enterococcus faecium. This study confirms that artisanal dairy fermentations are rich sources of LAB with robust gluten-degrading potential. The superior activity of Lactiplantibacillus spp. aligns with their complex peptidase systems. The geographical variation highlights the influence of local fermentation practices. Selected strains represent excellent candidates for developing adjunct cultures to produce gluten-reduced foods and warrant further investigation as potential probiotics, pending safety and efficacy validation in vivo and in clinical studies. Full article

Bacterial endophytes isolated from medicinal and wild plant species have recently gained significant attention for their medicinal properties, often closely linked to those of their plant hosts. This study identified two endophytic Bacillus isolates using 16S rRNA sequencing-based phylogeny. The impact of sublethal concentrations (0.5 mg/mL) of cadmium and hydrogen peroxide on metabolite production and bioactivity was also investigated. Phytochemical testing and antimicrobial and antioxidant assays revealed shifts in metabolite production under stress conditions. According to the phylogenetic analysis, Bacillus sp. NV35 and NV1 are respectively related to Bacillus cereus and B. mycoides. Phytochemical screening of methanolic crude extracts from both isolates tested positive for alkaloids, flavonoids, and saponins. Notably, tannins were detected only after cadmium treatment, while steroids were present following exposure to both cadmium and H₂O₂. LC-MS fingerprinting confirmed the presence of several tannins and steroids in treated samples. The untreated crude extracts exhibited an IC₅₀ of ~3 mg/mL with the DPPH assay, which decreased to ~1.5 mg/mL after treatment with cadmium or H₂O₂, demonstrating enhanced antioxidant potential under stress conditions. Additionally, extracts from both treated and untreated bacteria displayed antimicrobial activity against selected bacterial pathogens, with MIC values ranging from 62.5 μg/mL to 125 μg/mL. LC-MS analysis identified various antimicrobial and antioxidant metabolites, including phenoxymethylpenicilloyl, maculosin, (S,R,S)-alpha-tocopherol, 3-indoleacrylate, procyanidin A2, cis-11-eicosenamide, 3-hydroxy-3-phenacyloxindole, and 9-octadecenamide. Full article

Microbial biofertilizers offer a sustainable alternative to reduce inorganic fertilizer inputs in intensive vegetable production. While rhizobia are traditionally associated with legumes, their co-inoculation with native rhizobacteria for non-leguminous crops like tomatoes remains under-explored. This study aimed to isolate native rhizobacteria compatible with Bradyrhizobium diazoefficiens NE1-65 and evaluate their combined effect on the tomato plant (var. max F1) under reduced inorganic fertilizer rates. From the initial eighteen isolates screened on nitrogen-free media, and solubilization assays of phosphorus and potassium, three isolates (RM-8, RM-17, RM-18) were found compatible with B. diazoefficiens NE1-65. Isolate RM-17 (tentatively identified as Aureimonas sp. based on 16S rRNA gene sequence) was selected for its high K-solubilizing capacity (KSI = 8.60). Then, a 90-day growth trial compared various fertilizer application rates (0, 25, 50, 75, and 100%) with and without the bacterial consortia. The 75% fertilizer rate plus the consortia significantly outperformed the 100% fertilizer rate alone. Specifically, it increased plant height (11.57%), fruit diameter (9.23%), fruit number (53.90%), and fruit weight (16.15%). These findings demonstrate that the RM-17 and B. diazoefficiens NE1-65 consortia can partially substitute inorganic fertilizers while significantly enhancing tomato growth and yield, highlighting its potential application for sustainable tomato production systems. Full article

Well established long ago for bacterial and fungal detection, Matrix-Assisted Laser Desorption/Ionization–Time of Flight (MALDI-TOF) technique is not so well established in the virology field, and taking care of its advantages (speed, precision and low cost), this can be a powerful method for viral identification. To explore the feasibility and potential of MALDI-TOF for viral detection, this study shows the development of an in-house spectral library including several uninfected cell cultures and cultures infected with different clinically relevant viruses, such as SARS-CoV-2. This library was applied to the identification of viral infections directly on cell cultures, assessing the ability of the technique to discriminate between infected and non-infected profiles. Additionally, bioinformatic analyses were conducted to evaluate the structure, specificity, and reproducibility of the in-house library, and to understand its strengths and limitations. Sensitivity and specificity of the method were estimated by testing multiple culture batches from selected viruses included in the library. Together, these results provide a deeper understanding of the performance and applicability of MALDI-TOF in the virological context, highlighting its potential as a valuable research platform and a prospective tool for clinical viral detection. Full article

The excessive use of chemical fertilizers has depleted agricultural soils, necessitating a paradigm shift toward eco-friendly alternatives such as plant-beneficial microbes. However, the integration of plant-beneficial bacteria into global agroecosystems requires strategic and comprehensive analyses, as well as the development of optimally designed bioinocula to maximize their benefits. In this study, twenty-one rhizobacteria isolated from the maize rhizosphere were systematically screened for plant-beneficial traits, including phosphate and zinc solubilization, indole-3-acetic acid (IAA) production, and the synthesis of extracellular hydrolytic enzymes, followed by their evaluation for plant growth promotion. Among all bacterial isolates, Pseudomonas sp. NCR2 displayed the most comprehensive plant growth-promoting traits. In a pot-scale experiment, maize plants inoculated with multifaceted Pseudomonas sp. NCR2 showed significantly increased root growth, chlorophyll, soluble proteins, and phenolic contents as compared to untreated plants. This study underscores the significance of systematic screening of host-adaptive rhizobacteria for developing promising and tailored bioinocula. Furthermore, the results of this study also demonstrate the use of multifunctional biofertilizing inoculum for the systematic decrease of chemical inputs while simultaneously maintaining the crop productivity. Full article

Pest insect-associated microbes display great phenotypic and genotypic diversity, with many members inhabiting broader ecological niche. Several of these bacteria are ubiquitous in nature and contribute to fruit spoilage. When microbes occur in both environmental niches and insect hosts, their ability to adapt to diverse substrates may facilitate their ecological success. This study focuses on characterization of the metabolic capability of three bacterial isolates belonging to the genera Acetobacter and Pantoea associated with Drosophila suzukii collected in the Netherlands. Carbon utilization patterns and tolerance to environmental stressors were assessed under varying conditions of salinity, pH, and antibiotics. The isolates differed in their metabolic profiles but collectively demonstrated the capacity to utilize a wide range of carbon sources. In addition, they exhibited tolerance towards different chemicals including salt and antibiotics. The metabolic flexibility of bacteria associated with D. suzukii may facilitate their persistence within fruit environments and contribute to host ecology. Overall, this study provides functional insight into insect-associated bacteria and underscores the importance of metabolic characterization in understanding their ecological significance. Full article

(1) Background: Mammographic breast density (MBD) is a well-established predictor of breast cancer risk, yet the biological mechanisms underlying this association remain incompletely understood. MBD is characterized by alterations in breast stromal architecture, including increased collagen deposition and changes in immune cell composition. Given emerging evidence that the breast harbors a resident microbiome, we investigated whether the breast tissue microbiome correlates with MBD. (2) Methods: Adjacent normal breast tissue was collected under sterile conditions from 33 women undergoing surgery for benign or malignant breast disease. DNA was extracted and subjected to 16S rRNA gene sequencing (Illumina MiSeq). (3) Results: We observed a non-significant trend toward lower α-diversity in high-MBD samples compared to low-MBD samples, p = 0.13. β-Diversity analyses identified a modest association between MBD and microbial community composition (MiRKAT p = 0.049). A random forest-based model incorporating genus-level relative abundances improved prediction of MBD over clinical characteristics alone, identifying Corynebacterium (Actinobacteria) and other genera as key predictors. (4) Conclusions: Breast tissue microbial features vary with mammographic breast density, suggesting a potential association with density-associated breast cancer risk. These exploratory findings warrant validation in larger cohorts to better elucidate biological mechanisms and clinical relevance. Full article

Prophylactic antibiotic use in high-density ornamental aquaculture aims to mitigate infections, yet it is hypothesized to induce severe gut microbiome dysbiosis, contributing to high post-purchase mortality of goldfish purchased from retail stores by end consumers. This study utilized 16S rRNA gene amplicon sequencing, a rapid and high-resolution tool to characterize gut bacterial communities in six goldfish (Carassius auratus) sourced from antibiotic-intensive retail market in Hong Kong SAR, China. Diversity metrics were compared to unexposed reference controls and experimentally antibiotic-exposed cyprinid groups from published datasets. Market-sourced goldfish showed a profound collapse in alpha diversity (mean Shannon index 0.107 ± 0.141), far lower than controls (typically 2.0–4.5) and experimental groups (1.06–4.34). The microbiota exhibited extreme oligodominance by Cetobacterium and Vibrio, with near-total loss of beneficial commensal taxa. Principal coordinates analysis (PCoA) revealed distinct clustering, indicating fundamental and likely irreversible microbial restructuring. These findings show that chronic antibiotic exposure in ornamental supply chains induces a depauperate microbiome state, compromising host resilience and physiological homeostasis during environmental transitions. This dysbiosis provides a microbiological explanation for widespread post-purchase die-off, highlighting a major animal welfare and biosecurity concern. High-throughput sequencing offers quick, in-depth microbiome health assessment, essential for developing interventions to improve husbandry and reduce antimicrobial reliance in the global ornamental fish trade. Full article

The human oral cavity contains a variety of habitats, all of which are colonized by microorganisms. Oral bacteria form multi-genera communities, exhibiting adhesive properties, both to oral tissue surfaces and to each other. In certain conditions, these properties represent the first step towards the development of oral diseases. The oral microbiome undergoes changes in its composition, which can alter the balance between health and disease and is dynamically interconnected with the host. Probiotics with a targeted effect on the oral cavity can successfully compete with pathobionts and increase the presence of beneficial bacteria, thus contributing positively mainly to the prevention of oral diseases. The application of probiotics to maintain balance of oral microbiota has been a subject of intensive research. Oral health products containing lactic acid bacteria represent a modern approach to prevent or reduce the level of infections in the oral cavity. The application of these products is an alternative and promising way to prevent diseases through competitive interactions of beneficial microorganisms with pathobionts. Full article

In a changing climate, sustainable agriculture urgently requires environmentally friendly solutions. Increasing soil salinity severely limits crop productivity, as excess salts induce osmotic and ion-specific toxicity in plants. A promising strategy for mitigating these effects and enhancing plant salt tolerance involves the use of biofertilizers based on plant growth-promoting (PGP) rhizobacteria. In this study, novel salt-tolerant PGP strains were isolated and characterized from the rhizosphere of the halophyte Atriplex prostrata grown in soils with varying salinity levels. Twelve isolates were screened for key PGP traits, including indole-3-acetic acid (IAA) production, phosphate solubilization, siderophore synthesis, and NaCl tolerance. Two strains, AP9 and AP12, demonstrated the most comprehensive PGP potential. Based on 16S rRNA gene sequencing, they were identified as members of the genus Serratia. In an experiment under salt stress (75, 150, and 225 mM NaCl), inoculation of wheat (Triticum aestivum L.) seeds with these strains significantly improved germination rates and stimulated root and shoot development. The treated plants also exhibited reduced levels of key oxidative stress markers—malondialdehyde (MDA) and proline. Thus, the Serratia sp. AP9 and AP12 strains exhibit pronounced PGP activity and efficacy in enhancing the salt tolerance of wheat. These results indicate that these isolates are promising candidates for the development of novel biofertilizers for sustainable agriculture on saline soils. Full article

Mycobacteria form cellulose-containing biofilms and exhibit drug resistance at infection sites. However, the function of mycobacterial biofilms in host defense remains unclear. Herein, we demonstrate that reductive stress-induced mycobacterial biofilms evade macrophage capture and protect bacilli from nitric oxide stress. We first determined the optimal conditions for biofilm formation by mycobacteria. Using green fluorescent protein (GFP)-labeled mycobacteria, we then examined the protective effect of biofilms on the capture of bacilli by macrophages and found that macrophage capture was inhibited in the presence of biofilms. Furthermore, we constructed GFP-expressing mycobacteria that respond to acidic pH and nitric oxide stress, both of which are bactericidal factors. The results showed that mycobacterial biofilms protect bacilli from nitric oxide-mediated stress, but not from acidification. Finally, the removal of biofilms by cellulase enhanced the capture of mycobacteria by macrophages and the exposure of mycobacteria to nitric oxide. These findings highlight the protective roles of mycobacterial biofilms in innate immunity, particularly against macrophage capture and nitric oxide-induced stress. Full article