Viruses typically have high decay rates (mortality rates outside hosts), and applications of phage viruses for combating harmful bacterial in clinical and agricultural contexts would favor slow-decaying phage materials. There is evidence for a trade-off between viral survival and growth rate, which may constrain the evolution of reduced decay rate. Temperature is likely to affect the optimal balance of this trade-off; for example, faster growth may be more beneficial at warmer temperatures where phages spend less time outside of hosts in waiting for encountering a new host individual. We tested this hypothesis by experimentally evolving a lytic phage that infects the bacterium Pseudomonas fluorescens. Phages evolved at two temperatures for 20 cycles of dilution and propagation, with the ancestral bacteria being supplied every cycle. Phage populations from different temperatures showed different modes of adaptation in growth and decay traits. In particular, phages that evolved at the colder temperature showed a reduction in decay rate, regardless of assay conditions. Our results suggest phage training programs and resource collecting efforts to focus on cold environments for slow-decaying phage materials.

Methods to assure the health of crops owe their efficacy to the extent of which we understand the ecology and biology of environmental microorganisms, as well as the conditions under which their interactions can lead to losses in crop quality or yield. However, in the pursuit of this knowledge, notions of the ecology of plant-associated microorganisms have been reduced to an agro-centric focus. Microbial diversity is now known to be more diverse than previously thought in both environmental and host-associated habitats. This concept includes many lineages that are (or may become) host associated and can form part of pathobiomes, occasionally playing role in health condition of different plants. Surveys and samplings were conducted in natural habitats of Astragalus verus in Iran to monitor the status of prokaryotic agents associated with this herb. Two Gram-negative brownish-gray colored bacterial strains were isolated from plants, with symptoms suspected to presence of a living microorganism in two different sampling areas. The strains (namely D3 and M11) were identified as members of the genus Pseudomonas based on phenotypic features e.g., morphological characteristics, pigmentation, LOPAT scheme, etc. Precise phylogenetic position and taxonomic status of the strains were determined using the phylogeny of gyrB, rpoB and rpoD gene sequences. Accordingly, the two strains were classified within the Pseudomonas fluorescens subgroup in P. fluorescens lineage and clustered in a sister clade next to the type strain of Pseudomonas cedrina subsp. cedrina (DSM 17516). They were tested for sensitivity to copper compounds and various antibiotics with different targets and mechanisms of action. Additionally, the possibility of symptom development by these strains on some nearby and distant plants was investigated, and in many tested cases, some lesions were detected. Overall, these evidences suggest that A. verus may serve as a previously unreported ecological habitat for P. cedrina. It is hoped that this pioneering study of bacterial agents present in A. verus pathobiome will open up new horizons for investigating other existing agents associated with this herb, a plant species providing vital ecosystem functions for de-desertification, rangeland management and restoration, and yet less studied.

Pseudomonas fluorescens is a primary spoilage bacterium in aquatic products. Due to its strong ability to adhere to surfaces and form persistent biofilm, it poses a persistent challenge to food safety. Therefore, developing strategies to effectively inhibit biofilm formation holds significant research value. Dubosiella newyorkensis, a recently identified probiotic, has gained growing attention for its distinctive physiological features and potential functional benefits. Although various probiotic-derived cell-free supernatants (CFSs) have been explored for food preservation, the application of D. newyorkensis CFS against aquatic spoilage bacteria, and particularly its specific mechanism against P. fluorescens biofilm, has not been previously reported. Increasing evidence indicates that CFS from probiotic can influence microbial behavior, including biofilm development. In this study, we investigated the ability of D. newyorkensis CFS to inhibit P. fluorescens biofilm formation. The CFS treatment impaired bacterial growth and motility, lowered surface hydrophobicity, reduced self aggregation, and consequently hindered biofilm formation. Furthermore, CFS markedly decreased bacterial adhesion to food and contact surfaces. RT-qPCR analysis revealed that key genes associated with biofilm regulation were also significantly suppressed. Taken together, these results demonstrate that D. newyorkensis CFS exerts both antibacterial and antibiofilm effects against P. fluorescens. These findings provide a sound basis for exploring its application as a natural biopreservative to enhance the microbial safety and extend the shelf life of aquatic food products.

Adaptive evolution often leads to niche specialization, but successful colonization of a new niche can depend as much on ecological context as on genetic change. This is especially true in spatially structured environments, where the construction of habitat and order of arrival of mutants shape evolutionary outcomes. In static broth cultures, the air-liquid interface (ALI) provides a high-oxygen niche typically colonized by mat-forming strategists. In Pseudomonas fluorescens, single mutations that upregulate cellulose production give rise to 'wrinkly spreader' (WS) types-canonical niche specialists that out-compete ancestral types at the ALI. Here, we show that this view can be refined: WS mutants often fail to establish when introduced alone at low density, but co-culture with ancestral types rescues colonization. Microscopy and simulations reveal that ancestral types physically scaffold the ALI, enabling attachment and facilitating the in situ emergence of diverse WS mutants. Ancestral types later disperse, allowing WS expansion. This transient asymmetric interaction shows that even strongly adaptive mutations may rely on ecological facilitation. More broadly, our findings highlight the reciprocal links between ecology and evolution, revealing how transient ecological dependencies can shape adaptive trajectories.

Simultaneous biosurfactant production and bioremediation of polycyclic aromatic hydrocarbons and diesel fuel by a novel Pseudomonas fluorescens from Tunisian soil

Multi-substrate kinetic framework and wool-immobilised Pseudomonas fluorescens lipase (WPFL) for solvent-free biocatalysis of terpene esters from rose geranium oil

Abstract Salinity is a major abiotic stress limiting canola ( Brassica napus L.) productivity, especially in arid regions. This study aimed to evaluate the efficiency of plant growth-promoting rhizobacteria (PGPR) in enhancing early seedling tolerance to graded sodium chloride (NaCl) stress and to compare single- and multi-strain inoculations. A greenhouse experiment was conducted under NaCl concentrations ranging from 0 to 200 mM using three treatments: uninoculated control, single strain ( Bacillus subtilis , SB), and a triple-strain consortium ( Bacillus megaterium + Pseudomonas fluorescens + B. subtilis , TB). Growth, physiological, and biochemical traits were analysed, including relative water content (RWC), electrolyte leakage (EC), photosynthetic pigments, phenolic compounds, oxidative stress markers, and antioxidant enzyme activities such as superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). Salinity significantly reduced relative water content (RWC) from 60.10% to 48.63% and increased electrolyte leakage (EC) from 62.79% to 77.95%. TB inoculation mitigated these effects by maintaining higher RWC (53.57%) and lower EC (66.40%) than the control (71.93%). TB-treated plants showed higher chlorophyll (0.84 mg g⁻¹ FW), phenolics (10.34 mg GAE g⁻¹ DW ) , flavonoids (4.10 mg QE g⁻¹ DW ) , antioxidant capacity (85.98%), and proline (122.36 mg g⁻¹ FW ) compared to controls. Oxidative damage decreased, with hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) reduced to 14.01 µmol g⁻¹ FW and 60.22 nmol g⁻¹ FW, respectively. Enzymatic responses differed: SB enhanced SOD and CAT under moderate salinity, while TB increased POD and APX activities under mild stress. PGPR inoculation, particularly multi-strain consortia, alleviates salt-induced oxidative stress and improves osmotic adjustment and antioxidant defense in canola seedlings, offering an eco-friendly strategy for sustainable production in saline soils. Graphical Abstract

Cucumber (Cucumis sativus) belongs to the family Cucurbitaceae. Cucumbers are an important part of human diets as they contain essential vitamins, minerals and antioxidants. They are among the most significant commercial crops and are vital to the overall livelihood and food security of the people. They are well known for alleviating constipation, lowering blood sugar levels and treating jaundice, among health benefits. Cucumbers, however, are highly susceptible to attacks from various seed-borne pathogens. Seed-borne fungi such as Aspergillus niger (ITCC I.D. No. 11966.23) and A. flavus were identified from cucumber seeds through pathogenicity tests and cultural as well as morphological characterization. Among the ten fungicides tested, chlorothalonil exhibited the highest inhibition (100 %) A. niger, while Propiconazole was the most effective against A. flavus (100 %). Three bioagents were also evaluated, with Trichoderma harzianum showing the highest inhibition (64.52 %) for A. niger, while Pseudomonas fluorescens exhibited highest inhibition (53.74 %) for A. flavus. Eleven botanicals at 20 % concentration were tested and Allium sativum (garlic) demonstrated complete inhibition (100 %) against both A. niger and A. flavus. In growth promotion studies, it was observed that the pure culture of T. asperellum, when applied to cucumber seeds, resulted in the highest germination percentage (93.02 %), with greatest shoot length (18.59 cm) and the longest root length (6.67 cm). Overall, the study demonstrates that T. asperellum, A. sativum extract and selected fungicides can effectively manage seed-borne Aspergillus spp. while promoting cucumber seedling growth, highlighting their potential for integrated disease management strategies.

Tomato (Solanum lycopersicum) is a widely used vegetable in Ethiopia, but its production is severely affected by late blight, early blight and bacterial wilt. This study aims to isolate Pseudomonas fluorescens as a bio-control agent against Alternaria solani. Biological control using Pseudomonas fluorescens offers a potential alternative to chemical fungicides. Rhizosphere soil and healthy tomato roots were sampled from three Kebeles in North Wollo, Ethiopia. P. fluorescens was isolated on Pseudomonas Isolation Agar, while A. solani isolated from infected leaves on Potato Dextrose Agar and confirmed pathogenic on tomato seedlings. Three isolates of P. fluorescens (Pfs12, Pfk13, Pfsa31) were screened in vitro using the dual culture method, and their efficacy was further tested in vivo under greenhouse conditions. Isolates Pfs12 and Pfk13 showed moderate effectiveness against the radial growth of A. solani, achieving percent growth inhibitions of 56.04% and 55.04%, respectively. The standard chemical treatment (mancozeb) resulted in a 54.84% growth inhibition. The control group (Pseudomonas fluorescens) also demonstrated a moderate growth inhibition of 57.65% against A. solani. Data were gathered regarding disease parameters. The day after transplanting, the percent disease index was significantly lower in all treated groups compared to the control (water). The isolate Pfsa31 achieved the lowest disease index of 24.733%, which was comparable to the standard chemical treatment at 28.467%. Both treatments were significantly different from the control (water) at 60.333%. The findings showed the bio-control potential of selected P. fluorescens isolates as effective and environmentally sustainable alternatives to synthetic fungicides for the management of early blight disease in tomato cultivation, emphasizing the importance of utilizing indigenous strains for optimal performance.

Dual-species biofilm formation of Pseudomonas fluorescens and Hafnia alvei and their susceptibility to penicillin V acylase from Lactiplantibacillus plantarum YP4-1-2.

Abstract BACKGROUND Oxygen is a critical factor in shaping gut microbial communities and host-microbe interactions. In the healthy colon, the luminal environment is largely anaerobic, favoring strict anaerobes with beneficial functions. Inflammatory bowel disease (IBD) disrupts this balance. It has been proposed that epithelial damage and inflammation elevate local oxygen tension creating conditions that support facultative anaerobes associated with dysbiosis. Despite this, the ability of different gut bacteria to actively modulate oxygen levels remains poorly understood. Aim We aimed to systematically examine the ability of facultative anaerobic bacteria to deplete oxygen and generate localized anaerobic niches that may influence microbial ecology and inflammation in IBD. Methods & Results We cultured >60 gut-associated bacterial isolates, including Streptococcus, Enterococcus, Lactobacillus, Klebsiella, Pseudomonas, Acinetobacter, Enterobacter, Staphylococcus, Proteus, Listeria, Escherichia, Morganella, Serratia, Citrobacter, Salmonella, and Lactococcus species in a chemically defined medium ZMB1. Growth was monitored on a Synergy H1 plate reader, while oxygen was measured using a Resipher system. Whereas uninoculated controls maintained stable oxygen at ∼200 μM, multiple species, including Morganella morganii, Salmonella enterica, Pseudomonas fluorescens, P. aeruginosa, and Klebsiella spp. reduced oxygen concentrations to < 30 μM within 1 hr in an aerobic environment. Other strains, including Serratia marcescens, Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Proteus spp., Acinetobacter spp., and Enterococcus faecalis, quenched oxygen within 2 hours. The majority of these bacteria were able to maintain anaerobic conditions over 18 hrs. In contrast, most Streptococcus and Lactobacillus strains displayed little oxygen reduction. Genomic analysis revealed enrichment of cytochrome oxidases and nitrate/nitrite reductases among rapid oxygen consumers. Importantly, we demonstrated that the strict anaerobes Fusobacterium nucleatum and Clostridioides difficile could proliferate under aerobic conditions when co-cultured with oxygen-depleting bacteria. These co-cultures triggered heightened inflammatory responses, modeling how shifts in microbial oxygen metabolism could worsen mucosal inflammation. CONCLUSION We identify distinct gut microbes with the capacity to rapidly generate anaerobic microenvironments. In the context of IBD, where epithelial oxygenation is increased, these facultative anaerobes may play dual roles: promoting restoration of anaerobic niches that favor beneficial strict anaerobes, but also enabling the growth of pro-inflammatory taxa. Defining the oxygen-modulating capacity of gut bacteria provides a mechanistic foundation for understanding dysbiosis in IBD.

This critical review evaluates the synergistic potential of biochar, plant growth-promoting rhizobacteria (PGPR), and biological control agents (BCAs) for sustainable management of basal stem rot (BSR). Ganoderma boninense causes basal stem rot (BSR), a significant issue affecting oil palm (Elaeis guineensis L.) productivity, resulting in a 50-80% yield loss on approximately 400,000 hectares of oil palm in Southeast Asia. Chemical fungicides have drawbacks, including environmental degradation and pathogen resistance, which necessitate the development of sustainable alternatives. This review combines the information on the current literature on the use of biochar, plant growth-promoting rhizobacteria (PGPR), and biological control agents (BCAs) as a synergistic and environmentally friendly approach to the suppression of BSR. Biochar increases the soil structure, soil nutrient retention, and microbial habitats, whereas the PGPR increases the nutrient availability and systemic resistance. Biological control agents such as Trichoderma harzianum, Bacillus spp., and Pseudomonas fluorescens suppress Ganoderma boninense through mycoparasitism, antibiotic production, siderophore secretion, and induced systemic resistance. Integrated use of the triad has been reported to reduce BSR incidence by 40-70% and increase fresh fruit bunch yield by 15-35% in nursery and field trials. Nonetheless, there are still problems with dosage, compatibility, and scalability. Further improvements in efficacy are expected through optimization of biochar feedstock, selection and genetic enhancement of microbial strains, and precise timing and method of application, and site-specific formulations tailored to local soil and climate conditions.

This study evaluated the impact of location-specific improved production technology on the productivity and water use efficiency of Indian mustard (Brassica juncea (L.) Czern. & Coss.) grown on Old Alluvial Soils in the Eastern Indo-Gangetic Plains during the rabi seasons of 2022–23 and 2023–24, with the objective of promoting sustainable production management. The Indian mustard cultivar B-9 (Benoy) was cultivated in both years. The experiment comprised nine treatment combinations (T1–T9). Treatments T1–T8 incorporated improved production technologies, while T9 represented the control following traditional farmer practices. Treatment T8, involving seed treatment with Carbendazim, application of well-decomposed cow dung manure, Trichoderma viride, Pseudomonas fluorescens, recommended fertilizer dose, micronutrients, timely irrigation, residue retention, and integrated management of weeds, pests, and diseases, recorded the highest seed yield (1627and 1631 kg ha-1 in 2022–23 and 2023–24, respectively), reflecting 129.8% and 128.4% increases over the control. This treatment also provided 248.3% and 219.7% higher net returns over the control during the respective years, with benefit–cost ratios ranging from 1.91 to 1.97. Water use efficiency under T1–T8 (13.34–17.24 kg ha-1 mm-1) exceeded that of the control (10.14 kg ha-1 mm-1), demonstrating superior resource utilization and water savings. Overall, the integrated management approach employed in T8 proved agronomically effective, economically viable, and environmentally sustainable, presenting a promising pathway for enhancing mustard productivity, profitability, and resource-use efficiency in the studied agro-climatic zone.

Nanoarchitectonics of bacteriophage-based click fluorescent biosensing platform for detection of Pseudomonas fluorescens.

Three common agricultural beneficial microbes, Trichoderma harzianum, Bacillus cereus, and Pseudomonas fluorescens, are widely used in the growth cycle of crops, and increase the yield of agricultural products through disease prevention and sterilization. As a biodegradable biological macromolecular material, polylactic acid (PLA) is also widely used in agricultural production as a biodegradable film. The addition of agricultural microbes will affect the degradation rate of polylactic acid and thus its agricultural use. Under specific conditions (Tri15), the degradation rate of PLA film exceeds 30%. Scanning electron microscopy (SEM) images show that the degradation of the PLA happened after 360 days of exposure to these three specific microbe environments, which makes the surface of PLA films crack. Gel permeation chromatography (GPC) analysis reveals that in the presence of these microbes, the molecular weight of PLA is reduced. The analysis of 16S rDNA sequences demonstrates that the introduction of these microbes alters the soil microbial community, resulting in an enhanced abundance of Betaproteomicrobes, promoting the degradation of PLA. These results indicate that the three microbes species significantly promote the degradation of PLA, and the effects of microbes vary for the different concentrations. This study establishes practical guidelines for the deployment of PLA in real-world farmland environments.

Ecotoxicological insights into UV-P-induced immunotoxicity and bacterial infection risk in marine medaka (Oryzias melastigma).

Tomato pith necrosis is a damaging disease affecting greenhouse and field-grown tomato production globally, often associated with environmental stress and excessive nitrogen fertilization. This study investigates the bacterial etiology and the (inter)national context of disease outbreaks during the 2023–2024 growing seasons in Al Taif, Saudi Arabia (SA). Sixteen bacterial isolates were recovered from symptomatic plants, and phenotypic and molecular analyses identified Pseudomonas mediterranea (n = 12) and Pseudomonas viridiflava (n = 4) as the causal agents, although Pseudomonas corrugata and Pseudomonas fluorescens biotype I have also been reported from SA in the past. P. mediterranea was the most prevalent species, consistent with earlier findings in southern Europe. Genetic characterization using multilocus sequence typing and minimum spanning tree analysis revealed high genetic diversity in P. viridiflava, including a novel singleton lineage, indicating potential local adaptation, and all SA strains belonged to Pseudomonas syringae (sensu latu) phylogroup 7a. In contrast, P. mediterranea isolates exhibited lower genetic diversity, but six novel sequence types (ST8–ST13) were identified exclusively in SA strains, forming a distinct phylogenetic clade. Pathogenicity assays showed that P. viridiflava caused severe necrosis, while P. mediterranea caused internal browning without wilting, suggesting a difference in virulence. The co-occurrence of both species in the same greenhouses highlights the complexity of disease dynamics and potential interactions between these pathogens. Given the global relevance of P. syringae phylogroup 7a, mainly formed by P. viridiflava strains, and the risk of pathogen spread via plant trade, this study underscores the importance of stringent phytosanitary controls and accurate diagnostics tailored to regional pathogen variants.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-33480-y.

Biofilm-forming bacteria, such as Bacillus cereus and Vibrio harveyi are major contributors to food contamination and problems in aquaculture. This study aimed to evaluate the antibiofilm compounds of the phyllosphere bacterial supernatants (Pseudomonas fluorescens JB 3B and Proteus myxofaciens JB 20B), bacteriophages (BC-VP and Vh-S4-phage), and their combinations against these pathogens. Antibacterial and quorum sensing assays showed no activities. The combination of antibiofilm compounds and bacteriophages revealed measurable but species-dependent effects. For B. cereus, the JB 3B-phage and JB 20B-phage combinations revealed inhibition results of 39.21% and 39.62%, and destruction results of 50.60% and 43.12%, respectively. In contrast, V. harveyi showed much lower responses, with inhibition results at 3.49% and 4.80%, and destruction at 9.28% and 6.39%, respectively. SEM analysis supported the microscopic observations, showing reduced biofilm layers and disrupted biofilm matrix structures in treated groups. Gas chromatography - mass spectrometry (GC-MS) analysis showed potential antibiofilm compounds, including acetic acid, sarcosine, 4-octadecenal, and erythritol. Statistical analysis confirmed significant effects of bacterial species, treatment, and the interaction on both biofilm inhibition and destruction (p < .05). Overall, the study highlights specific phyllosphere-derived compounds and bacteriophages with promising antibiofilm activity, while emphasizing that their combined use may not always enhance efficacy in controlling biofilm-related contamination in aquaculture and food industry.

ABSTRACTMedicinal plants such as Centella asiatica, Conyza sumatrensis, and Justicia betonica are widely used in Uganda for traditional wound healing. However, the impact of cultivation conditions on their therapeutic potential remains poorly understood. This study compared the phytochemical profiles and bioactivities of hydroponically cultivated and wild‐collected material of these species from Lugazi Diocese, Uganda. Extracts were prepared using ethanol, methanol, and water, and analyzed by thin‐layer chromatography (TLC), high‐performance liquid chromatography (HPLC‐UV), headspace gas chromatography–mass spectrometry (HS‐GC–MS), and liquid chromatography–tandem mass spectrometry (LC–MS/MS). TLC and HPLC‐UV indicated terpenoids, flavonoids, and steroids, while HS‐GC–MS revealed predominantly monoterpenes and sesquiterpenes. LC–MS/MS annotated flavonoids, including quercetin‐3‐O‐glucuronoside, kaempferol‐3‐O‐rutinoside, and kaempferol, as well as triterpenoids such as asiatic acid and katononic acid. Antibacterial activity was evaluated against Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, and Saccharomyces cerevisiae using the agar well diffusion method. Anti‐inflammatory effects were assessed by IL‐6 and IL‐8 secretion, and cytotoxicity by MTT assay. Ethanol and methanol extracts exhibited moderate antibacterial activity, while aqueous extracts of wild C. asiatica and hydroponic C. sumatrensis significantly reduced IL‐6 secretion. No cytotoxic effects were detected. These findings suggest hydroponic cultivation preserves essential phytochemicals and bioactivities, supporting sustainable production of medicinal plants for therapeutic applications.

Neutralization Mechanism of a HipA-like Toxin Targeting Isoleucyl-tRNA Synthetase.