Cerium oxide nanoparticles (CeO2NPs) possess unique physicochemical properties that make them promising compounds for medical and industrial applications. However, variations in synthesis methods, particle size, and surface characteristics may influence their potential toxicity. This study provides a comparative analysis of CeO2NPs synthesized via three methods (citric, dextran, and uncoated modifications) to evaluate their toxicity, antioxidant mechanisms, and genoprotective potential using a panel of Escherichia coli-based lux-biosensors. Our data indicate that all of the tested CeO2NPs exhibit high biocompatibility with no significant toxicity or genotoxicity at physiological concentrations (10-4-10-2 M). The citrate-modified nanoparticles demonstrated pronounced catalase-mimetic activity, acting as the most effective scavengers against hydrogen peroxide. Conversely, the dextran-modified nanoparticles exhibited the highest antimutagenic potential, reducing dioxidine-induced DNA damage by over 56%. Thus, beyond establishing biocompatibility, this study highlights the potential of using specific CeO2NP modifications for targeted therapy depending on the oxidative pathway involved. This suggests their potential for application as antioxidant and antimutagenic agents in both human and veterinary medicine.

Applying quorum-quenching (QQ) probiotics is a promising non-antibiotic-based strategy for sustainable aquaculture. In this study, a total of fifty-two Streptomyces strains were isolated and identified from aquaculture pond sediment and intestines of fish collected in the Panyu District of Guangzhou, China. Half of the isolated strains exhibited varying degrees of antagonistic activity against a variety of pathogenic bacteria in aquaculture, including Aeromonas hydrophila, Pseudomonas aeruginosa, Vibrio parahemolyticus, Staphylococcus aureus, and Streptococcus agalactiae. Among the forty-four strains whose genome was successfully isolated, 39 (similar to 90 %) were demonstrated carrying AHL-acylase encoding genes by PCR, indicating the natural and ubiquitous potential of Streptomyces spp. in degrading quorum sensing (QS) signals. Nine strains, S7, S10, S11, S25, TI9, TI11, TI15, DI5, and DI9, showed clear QS inhibition (QSI) activity in agar well diffusion assays by applying Agrobacterium tumefaciens A136 and Chromobacterium violaceum CV026 as biosensors. An RT-PCR analysis demonstrated the repressed expression of a variety of virulence genes in P. aeruginosa when co-cultured with strain S25. The results of this study demonstrate the favorable probiotic potential of Streptomyces spp. Isolated from the aquaculture environment, particularly in their ubiquitous QSI ability. These strains serve as promising QQ probiotic candidates and may contribute to developing novel eco-friendly anti-virulence therapy strategies for aquaculture.

Aquaculture is central to global food security, but intensification of production has increased disease risk and environmental pressure. The gut microbiome of aquatic organisms is now recognized as a key mediator of host physiology, nutrition, immunity, and pathogen resistance, making it a promising alternative to antimicrobial-based disease control. This review summarizes current knowledge on the composition, assembly, and functional roles of the gut microbiome in fish and crustaceans of aquacultural importance. Major bacterial phyla include Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia. Community structure is shaped by environment, diet, host age, genetics, stress, and stochastic processes, with differences between marine and freshwater systems. The microbiome contributes to immune defense through short-chain fatty acid production, Toll-like receptor signaling, cytokine regulation, mucosal immunoglobulin responses, antimicrobial peptide and bacteriocin production, and competitive exclusion of pathogens. It also supports productivity by improving nutrient assimilation, vitamin and enzyme synthesis, and feed conversion. Probiotics, prebiotics, and synbiotics are discussed as strategies for targeted microbiome modulation, although unstable colonization and the lack of standardized protocols remain major challenges. Overall, targeted microbiome manipulation offers a promising route toward sustainable, antimicrobial-reduced aquaculture.

Hibernation induces significant physiological changes in mammals, including suppressed immune responses, metabolic downregulation, and shifts in gut microbiota activity. This study examined seasonal variation in the functional properties of gut microbiota in Nyctalus noctula by assessing the genotoxic and oxidative effects of microbial metabolites using lux-biosensor assays based on Escherichia coli strains carrying stress-inducible promoters: PrecA for detecting DNA damage responses and PkatG for oxidative stress responses. Fifty-eight microbial isolates were obtained from fecal samples collected during hibernation (n = 26) and active (n = 32) periods and evaluated for mutagenic, DNA-protective, antioxidant, and prooxidant activities. Metabolites from isolates collected during hibernation exhibited significantly stronger DNA-protective effects compared to those from active bats, while oxidative stress modulation did not differ significantly between the two groups. A significant negative correlation was observed between bacterial abundance and antioxidant responses, suggesting a possible link between microbial density and functional activity. These results indicate that the physiological state of the host influences the functional output of gut microbiota, particularly in relation to DNA protection. The findings enhance our understanding of seasonal microbiome–host interactions in bats and underscore the relevance of microbial metabolites in shaping host stress responses during hibernation.

Self-assembling antimicrobial complexes are a promising new technology for the development of antimicrobial, antifungal, and other bioactive agents with targeted delivery, adaptability, and the regulation of processes over time. Ribosomally synthesized antimicrobial peptides (AMPs) are most frequently considered as the basis for such complexes; however, we suggest that non-ribosomally synthesized peptides (NRPs) should be considered as molecules that also hold potential for engineering and already possess a set of qualities that AMPs are still to be engineered to have. This review examines the key features of NRP structure and self-assembly that determine their potential as antimicrobial agents, as well as NRP engineering methods through which new, more advanced agents for combating antibiotic-resistant microorganisms can be created.

During a screening for potential probiotics for aquaculture, several Bacillus strains with enzymatic and antioxidant activity were isolated. Following cross-antagonistic activity assays, two pairs of strains were prioritized: Bacillus velezensis MT14 and MT42, which displayed both proteolytic and amylolytic functions, and Bacillus subtilis MT48 and MT74, which additionally demonstrated antioxidant capacity. Potential probiotic strains were introduced into starter feeds for sterlet larvae for 2 months. Both experimental groups demonstrated weight gain compared to the control. The proportion of fish with higher weight increased by 9.65% in Group 1 and by 14.75% in Group 2. A reduction in IL-1β gene expression occurred in both groups, suggesting a reduction in inflammation. Group 2 exhibited decreased expression of IGF-1, HSP 70, and GST genes, which may indicate a positive impact of the antioxidant activity of the potential probiotic on alleviating stress. Genomic sequencing revealed that only the strains with antioxidant activity possessed genes coding pulcherriminic acid, bacillibactin, subtilosin, and fengicin synthetases-a feature absent in other strains. This finding implies that these metabolites, especially pulcherriminic acid, may contribute to the antioxidant properties of these strains. These results highlight the importance of considering strain-specific characteristics when developing probiotics tailored to the requirements of aquaculture.

Zinc (Zn) is a vital micronutrient required for optimal plant growth and soil fertility. Its use in the form of nanoparticles (NPs) has gained significant attention in agricultural applications. Green synthesized Zn-based NPs offer an eco-friendly solution to several conventional problems in agriculture. Several plants, bacteria, fungi and yeast have shown significant potential in fabricating Zn NPs that can provide environmentally friendly solutions in agriculture and the approach is aligned with sustainable agricultural practices, reducing the dependency on harmful agrochemicals. Zn-based NPs act as plant growth promoters, enhance crop yield, promote resilience to abiotic stressors and are efficient crop protection agents. Their role as a smart delivery system, enabling targeted and controlled release of agrochemicals, further signifies their potential use in agriculture. Because agriculture requires repeated applications hence, the toxicological aspects of Zn NPs cannot be ignored. Zn NPs are reported to cause phytotoxicity, including root damage, physiological and biochemical disturbances, and genotoxic effects. Furthermore, exposure to Zn NPs poses risks to soil microbiota, and aquatic and terrestrial organisms potentially impacting the ecosystem. The green synthesis of Zn-based NPs has a promising aspect for advancing sustainable agriculture by reducing agrochemical use and improving crop productivity. Their diverse applications as plant growth promoters, crop protectants and smart delivery systems emphasize their potential. However, the toxicological aspects are essential to ensure the standardization of doses for their safe and effective use. Further research would help address such concerns and help in developing viable and eco-friendly solutions for modern agriculture. © 2025 Society of Chemical Industry.

Aquaculture is one of the fastest-growing sectors in food production. The widespread use of antibiotics in fish farming has been identified as a driver for the development of antibiotic resistance. One of the promising approaches to solving this problem is the use of probiotics. There are many promising aquaculture probiotics in the Bacillus genus, which produces non-ribosomal peptides (NRPs). NRPs are known as antimicrobial agents, although evidence is gradually accumulating that they may have other effects, especially at lower (subinhibitory) concentrations. The mechanisms of action of many NRPs remain unexplored, and molecular docking and molecular dynamics studies are invaluable tools for studying such mechanisms. The purpose of this study was to investigate the in silico inhibition of crucial bacterial targets by NRPs. Molecular docking analyses were conducted to assess the binding affinities of the NRPs of Bacillus for protein targets. Among the complexes evaluated, bacillibactin with glutamine synthetase, dihydrofolate reductase, and proaerolysin exhibited the lowest docking scores. Consequently, these complexes were selected for further investigation through molecular dynamics simulations. As a result, three additional potential mechanisms of action for bacillibactin were identified through in silico analyses, including the inhibition of glutamine synthetase, dihydrofolate reductase, and proaerolysin, which are critical bacterial enzymes and considered as the potential antibacterial targets. These findings were further supported by in vitro antagonism assays using bacillibactin-producing Bacillus velezensis strains MT55 and MT155, which demonstrated strong inhibitory activity against Pseudomonas aeruginosa and Aeromonas veronii.

Aquaponics is an integrated method of aquatic animal and plant cultivation in a closed recycling system where the wastewater from aquatic animals is purified by microbes, which transform pollutants into nutrients for plants at the end of the chain. This technology allows to the efficiency of the area to be increased by a combination of cultivated plants and aquatic animals. Aquaponics produces environmentally friendly products by reducing fertilizer use and wastewater volume, increasing the extent of reuse by up to >90%. A promising way to increase efficiency in aquaponics is to use bacterial preparations (probiotics). This will allow control of the development of pathogens in the growing system, improving water quality and the growth rate of aquatic organisms. This paper overviews the experience of using probiotic preparations in aquaponic systems. It is shown that probiotics are able to increase the survival rate of aquatic organisms, improve the hydrochemical regime in recirculating aquaculture systems, and mitigate the risk of pathogenic contamination. There are a number of problems in aquaponics that prevent it from becoming more widespread and achieving maximum productivity, including problems with optimal pH and temperature, problems with nutrient and oxygen depletion, as well as diseases caused by phytopathogens and fish pathogens. The probiotics used do not take into account the biological needs of all components of the aquaponic system. The development of probiotic preparations from soil bacteria of the genus Bacillus will allow us to create a new class of probiotics specifically for aquaponics. Such preparations will work in a wide pH range, which will allow us to achieve maximum productivity for all components of aquaponics: animals, plants and bacteria.

This work is a systematic review of current scientific concepts regarding the mechanisms of formation and control of the rhizosphere microbiota by plants. The main pathways of plant influence on the composition and functional activity of root-associated microbial communities are analyzed. The structural organization of the rhizosphere is considered, with three main zones distinguished: the endorhizosphere, rhizoplane, and ectorhizosphere, each characterized by a specific composition of microorganisms. The mechanisms for attracting beneficial microorganisms through the production of root exudates, including amino acids, sugars, organic acids, vitamins, and phenolic compounds, are described. It is shown that plants can selectively attract specific bacterial taxa through species-specific chemical signals and chemotaxis. The processes of bacterial attachment to the root surface involving adhesins, protein appendages, and exopolysaccharides, leading to the formation of biofilms, are examined. The role of phytohormones in regulating the microbiota composition, including strigolactones, abscisic, indoleacetic, jasmonic, and salicylic acids, is analyzed. Data on the genetic determinism of plant-microorganism interactions and the differences between wild and cultivated plant forms in the formation of the rhizobiome are presented. Current views of the rhizosphere as a dynamic system with multiple feedback loops between the plant and the microbiota are summarized. Practical recommendations for the selection of phytostimulant bacteria for agricultural purposes, based on an understanding of the principles of plant-microbial interactions, are formulated.

This work is aimed at studying the effects of rifampicin resistance mutations on the synthesis of secondary metabolites with antioxidant and DNA-protective properties. We used probiotic strains of the genus Bacillus : B. amyloliquefaciens B-1895 and B. subtilis KATMIRA1933. The antioxidant, DNA-protective activity, and the ability to suppress the SOS-response in B. amyloliquefaciens B-1895 and B. subtilis KATMIRA1933 rifampicin-resistant mutants have been studied for the first time. It has been found that antioxidant, DNA protective, and SOS-inhibiting activity is higher in rifampicin-resistant mutants than that of original strains. According to the study results, it has been discovered that the antioxidant, DNA-protective and SOS-inhibitory activity in mutants B. amyloliquefaciens B-1895 and B. subtilis KATMIRA1933 resistant to rifampicin is higher than in control strains, which indirectly proves the pleiotropic effect of the rpoB gene on these activities.

The article is a brief literature review. This article provides an overview of the Quorum Sensing system in bacterial communities, highlighting the peculiarities of the system for gram-positive and gramnegative microorganisms. Basic information about the three existing Quorum Sensing systems is presented. Information is also given about different types of autoinducers, which are signaling molecules that trigger a cascade of behavioral reactions. The importance of the Quorum Sensing system as one of the fundamental mechanisms in the formation and regulation of bacterial biofilms is described, emphasizing the significance of biofilm microorganisms for modern clinical medicine and their impact on aggravating the issue of antibiotic resistance. The main mechanisms of inhibiting bacterial quorum, including by other microorganisms, are presented. The work discusses enzymatic and non-enzymatic methods of inhibiting the Quorum Sensing system, points of application and mechanisms of action. Some microorganisms with confirmed enzymatic activity by Quorum Quenching are indicated. Also presented are registered cases of suppression of other bacteria by microorganisms through the Quorum Sensing inhibitors system.

Probiotics, due to their multifaceted benefits to the host, are essential in medicine, agriculture, and aquaculture. The mechanisms of their action at the molecular level are complex and less explored. Both previous research and our own investigations have highlighted that incorporating probiotics into the feed of commercial fish can increase growth and influence the expression of genes related to stress and immunity. Additionally, probiotics with antioxidant properties often exert systemic effects. The aim of this work was to explore possible mechanisms of probiotic effects on stress-related proteins in African catfish C. gariepinus using molecular docking and dynamics approaches. Stress biomarker proteins such as catalase, cytochrome P450, HSP70, metallothionein 1, and superoxide dismutase were evaluated for possible interactions with bioactive non-ribosomal peptides (NRPs) from Bacillus subtilis R5, used as ligands. The study involved molecular docking and dynamics interactions between proteins and NRPs. The results of molecular docking and dynamics reveal multiple bindings between proteins and ligands, forming stable complexes, which may explain the mechanisms of action of probiotics and their particularly positive effects, such as the reduction in stress levels, which was demonstrated in the clarium catfish model in our previous work. Non-ribosomal peptides synthesized by probiotics may influence key signalling pathways underlying antioxidant and antimutagenic properties.

Root architecture has a key role in influencing plant growth and yield. In recent years, the agriculture sector has gained interest in harnessing the potential of plant growth-promoting rhizobacteria (PGPR) that possess the competence to produce phytohormones, with the aim of enhancing these desirable traits. Phytohormone-producing PGPR exert their influence on root development through the modulation of phytohormone production and distribution, encompassing auxins, cytokinins, and gibberellins. These beneficial bacteria stimulate lateral root proliferation, elongate root hairs, and promote the accumulation of root biomass, ultimately leading to heightened nutrient uptake and enhanced water absorption. Moreover, the phytohormones synthesized by PGPR serve to activate stress signalling pathways, thereby strengthening plant resilience against an abiotic stressor, viz., drought, heavy metal, salinity, and toxicity.This comprehensive review article highlights the role of these PGPR and their significant impact on augmenting root architecture in plants. The development of roots is often vulnerable to several abiotic factors, which in turn adversely affects the initial growth and overall health of the plants. This review thoroughly explores the complex interaction of phytohormones in mitigating abiotic stresses through their modulation of root development. Additionally, the interaction between phytohormone-producing PGPR and nanoparticles (NPs) has emerged as a significantly promising approach to reinforce plant growth and an ability to improve the colonization and activity of PGPR in the rhizosphere, further expanding their beneficial effects on root architecture and stress tolerance. Within this context, we have discussed the stimulating dynamics of PGPR interaction with NPs in sustaining root architecture to optimize plant health and effectively mitigate abiotic stresses.

Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the “familiarity of conditions” hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Bacteria of the genus Bacillus are known for their ability to suppress a wide range of pathogenic microflora through the production of a variety of secondary metabolites, a significant proportion of which are non-ribosomal peptides. The importance of selecting conditions for the most efficient synthesis of non-ribosomal peptides is related to this. The influence of cultivation conditions can be assessed by analyzing the gene expression of non-ribosomal peptide synthetases of target NRPs and studying the mechanisms of its regulation. The aim of this study is to investigate the influence of growth medium composition on the expression of non-ribosomal peptide synthetase genes in Bacillus bacteria.

The potential probiotic properties of three Bacillus strains were studied. A probiotic supplement for the African catfish Clarias gariepinus was produced via the solid-state fermentation protocol and incorporated into the fish feed for a period of seven weeks. Since the 36th day of the experiment, all experimental groups had a statistically significant increase in their weight gain than the control group. The maximum weight gain observed in fish fed the probiotic-supplemented feed was 29.16% higher than that of the control group, and the maximum feed conversion rate improvement was 24%. Cell-free extracts from these strains showed antioxidant (11.55–27.40%) and DNA-protective (45.33–61.83%) activity in a series of in vitro biosensor tests. Further investigation into the antimutagenic activity of the strains revealed that two of them reduced the level of induced mutagenesis in an Escherichia coli model (by 33.58% and 54.35%, respectively). We also assessed the impact of probiotic strains on the expression of several key genes in the host (C. gariepinus), including hsp70, cxc, tnfα, il1β, and lysC. More than a 10-fold increase in expression rates was observed for hsp70 in gonads and liver; for cxc in muscles and gonads; for tnfα in brain, gills, and liver; for il1β in the brain, gills, gonads, and liver; and for lysC in gills, gonads, liver, and muscles. This study provides evidence that probiotics exhibiting antioxidant and antimutagenic properties can provide significant benefits in vivo within aquaculture systems. The molecular effects of these probiotics appear to be complex and tissue-specific, with both upregulation and downregulation of immune system genes observed. Nevertheless, at the organismal level, the impact was unequivocally positive in terms of aquaculture objectives, manifested as enhanced body weight gain in the fish. Consequently, these Bacillus strains warrant serious consideration as potential probiotics for this species.