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Background/Objectives: Antimicrobial resistance (AMR) contributes to millions of deaths globally each year, creating an urgent need for new therapeutic agents. Antimicrobial peptides (AMPs) have emerged as promising candidates due to their potential to combat AMR pathogens. This study aimed to evaluate the antimicrobial activity of an AMP from a soil-derived bacterial isolate against Gram-negative bacteria. Method: Soil bacteria were isolated and screened for antimicrobial activity. The bioactive peptide was purified and determined its structure and antimicrobial efficacy. Genomic analysis was conducted to predict the biosynthetic gene clusters (BGCs) responsible for AMP production. Results: Genomic analysis identified the isolate as Paenibacillus sp. Na14, which exhibited low genomic similarity (61.0%) to other known Paenibacillus species, suggesting it may represent a novel species. The AMP from the Na14 strain exhibited heat stability up to 90 °C for 3 h and retained its activity across a broad pH range from 3 to 11. Structural analysis revealed that the Na14 peptide consisted of 14 amino acid residues, adopting an α-helical structure. This peptide exhibited bactericidal activity at concentrations of 2–4 µg/mL within 6–12 h, and its killing rate was concentration-dependent. The peptide was found to disrupt the bacterial membranes. The Na14 peptide shared 64.29% sequence similarity with brevibacillin 2V, an AMP from Brevibacillus sp., which also belongs to the Paenibacillaceae family. Genomic annotation identified BGCs associated with secondary metabolism, with a particular focus on non-ribosomal peptide synthetase (NRPS) gene clusters. Structural modeling of the predicted NRPS enzymes showed high similarity to known NRPS modules in Brevibacillus species. These genomic findings provide evidence supporting the similarity between the Na14 peptide and brevibacillin 2V. Conclusions: This study highlights the discovery of a novel AMP with potent activity against Gram-negative pathogens and provides new insight into conserved AMP biosynthetic enzymes within the Paenibacillaceae family. Full article

One hundred presumptive Pseudomonas isolates, recovered from 15 sites impacted by anthropogenic activity in the Foggia district (Italy), were screened for key adaptive and functional traits important for environmental applications. The isolates were phenotypically characterized for their ability to grow under combined pH (5.0–8.0) and temperature (15–37 °C) conditions, to produce proteolytic enzymes, pigments, and exopolysaccharides, and to tolerate SDS. Moreover, the resistance to six environmentally relevant heavy metals (Cd, Co, Cu, Ni, Zn, As) was qualitatively assessed. The results highlighted wide inter-strain variability, with distinct clusters of isolates showing unique combinations of stress tolerance, enzymatic potential, and resistance profile. PERMANOVA analysis revealed significant effects of both the isolation site and the metal type, as well as their interaction, on the observed resistance patterns. A subset of isolates showed co-tolerance to elevated temperatures and heavy metals. These findings offer an initial yet insightful overview of the adaptive diversity of soil-derived Pseudomonas, laying the groundwork for the rational selection of strains for bioaugmentation in contaminated soils. Full article

The rhizosphere microbiome plays an important role in carbon- and nitrogen-cycling in soil and in the stress response of plants. It also affects the function of the ammonium transporter (AmtB) that senses nitrogen levels inside and outside the cells of the associative nitrogen-fixing bacterium GXGL-4A. However, the potential mechanism of the interaction between the AmtB deletion mutant of GXGL-4A (∆amtB) and microorganisms in the rhizosphere of plants under low-nitrogen stress is still unclear. As revealed by transcriptome analyses, mutation of the amtB gene in GXGL-4A resulted in a significant up-regulation of many functional genes associated with nitrogen fixation and transportation at transcription level. The application of ∆amtB changed the nitrogen level in the rhizosphere of cucumber seedlings and reshaped the microbial community structure in the rhizosphere, enriching the relative abundance of Actinobacteriota and Gemmatimonadota. Based on bacterial functional prediction analyses, the metabolic capacities of rhizobacteria were improved after inoculation of cucumber seedlings with the original strain GXGL-4A or the ∆amtB mutant, resulting in the enhancement of amino acids, lipids, and carbohydrates in the cucumber rhizosphere, which promoted the growth of cucumber plants under a low-nitrogen stress condition. The results contribute to understanding the biological function of gene amtB, revealing the regulatory role of the strain GXGL-4A on cucumber rhizosphere nitrogen metabolism and laying a theoretical foundation for the development of efficient nitrogen-fixing bacterial agents for sustainable agricultural production. Full article

Soil salinization severely restricts crop growth and presents a major challenge to global agriculture. In this study, a plant-growth-promoting rhizobacterium (PGPR) was isolated and identified as Proteus sp. through 16S rDNA analysis and was subsequently named Proteus sp. JHY1. Under salt stress, exogenous dopamine (DA) significantly enhanced the production of indole-3-acetic acid and ammonia by strain JHY1. Pot experiments revealed that both DA and JHY1 treatments effectively alleviated the adverse effects of 225 mM NaCl on rice, promoting biomass, plant height, and root length. More importantly, the combined application of DA-JHY1 showed a significant synergistic effect in mitigating salt stress. The treatment increased the chlorophyll content, net photosynthetic rate, osmotic regulators (proline, soluble sugars, and protein), and reduced lipid peroxidation. The treatment also increased soil nutrients (ammoniacal nitrogen and available phosphorus), enhanced soil enzyme activities (sucrase and alkaline phosphatase), stabilized the ion balance (K⁺/Na⁺), and modulated the soil rhizosphere microbial community by increasing beneficial bacteria, such as Actinobacteria and Firmicutes. This study provides the first evidence that the synergistic effect of DA and PGPR contributes to enhanced salt tolerance in rice, offering a novel strategy for alleviating the adverse effects of salt stress on plant growth. Full article

Heavy metal pollution represents a pervasive environmental challenge that significantly exacerbates the ever-increasing crisis of antimicrobial resistance and the capacity of microorganisms to endure and proliferate despite antibiotic interventions. This review examines the intricate relationship between heavy metals and AMR, with an emphasis on the underlying molecular mechanisms and ecological ramifications. Common environmental metals, including arsenic, mercury, cadmium, and lead, exert substantial selective pressures on microbial communities. These induce oxidative stress and DNA damage, potentially leading to mutations that enhance antibiotic resistance. Key microbial responses include the overexpression of efflux pumps that expel both metals and antibiotics, production of detoxifying enzymes, and formation of protective biofilms, all of which contribute to the emergence of multidrug-resistant strains. In the soil environment, particularly the rhizosphere, heavy metals disrupt plant–microbe interactions by inhibiting beneficial organisms, such as rhizobacteria, mycorrhizal fungi, and actinomycetes, thereby impairing nutrient cycling and plant health. Nonetheless, certain microbial consortia can tolerate and detoxify heavy metals through sequestration and biotransformation, rendering them valuable for bioremediation. Advances in biotechnology, including gene editing and the development of engineered metal-resistant microbes, offer promising solutions for mitigating the spread of metal-driven AMR and restoring ecological balance. By understanding the interplay between metal pollution and microbial resistance, we can more effectively devise strategies for environmental protection and public health. Full article

Flavonoids serve as crucial plant antioxidants in drought tolerance, yet their antioxidant regulatory mechanisms within mycorrhizal plants remain unclear. In this study, using a two-factor design, trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings in the four-to-five-leaf stage were either inoculated with Funneliformis mosseae or not, and subjected to well-watered (70–75% of field maximum water-holding capacity) or drought stress (50–55% field maximum water-holding capacity) conditions for 10 weeks. Plant growth performance, photosynthetic physiology, leaf flavonoid content and their antioxidant capacity, reactive oxygen species levels, and activities and gene expression of key flavonoid biosynthesis enzymes were analyzed. Although drought stress significantly reduced root colonization and soil hyphal length, inoculation with F. mosseae consistently enhanced the biomass of leaves, stems, and roots, as well as root surface area and diameter, irrespective of soil moisture. Despite drought suppressing photosynthesis in mycorrhizal plants, F. mosseae substantially improved photosynthetic capacity (measured via gas exchange) and optimized photochemical efficiency (assessed by chlorophyll fluorescence) while reducing non-photochemical quenching (heat dissipation). Inoculation with F. mosseae elevated the total flavonoid content in leaves by 46.67% (well-watered) and 14.04% (drought), accompanied by significantly enhanced activities of key synthases such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), 4-coumarate:coA ligase (4CL), and cinnamate 4-hydroxylase (C4H), with increases ranging from 16.90 to 117.42% under drought. Quantitative real-time PCR revealed that both mycorrhization and drought upregulated the expression of PtPAL1, PtCHI, and Pt4CL genes, with soil moisture critically modulating mycorrhizal regulatory effects. In vitro assays showed that flavonoid extracts scavenged radicals at rates of 30.07–41.60% in hydroxyl radical (•OH), 71.89–78.06% in superoxide radical anion (O₂^•−), and 49.97–74.75% in 2,2-diphenyl-1-picrylhydrazyl (DPPH). Mycorrhizal symbiosis enhanced the antioxidant capacity of flavonoids, resulting in higher scavenging rates of •OH (19.07%), O₂^•− (5.00%), and DPPH (31.81%) under drought. Inoculated plants displayed reduced hydrogen peroxide (19.77%), O₂^•− (23.90%), and malondialdehyde (17.36%) levels. This study concludes that mycorrhizae promote the level of total flavonoids in trifoliate orange by accelerating the flavonoid biosynthesis pathway, hence reducing oxidative damage under drought. Full article

Oxybenzone (OBZ), an organic ultraviolet filter, is an emerging contaminant posing severe threats to ecosystem health. Using tobacco (Nicotiana tabacum) as a model plant, this study investigated the alleviation mechanisms of exogenous silicon (Na₂SiO₃, Si) and bamboo-based biochar (Bc) under OBZ stress. We systematically analyzed physiological and biochemical responses, including phenotypic parameters, reactive oxygen species metabolism, photosynthetic function, chlorophyll synthesis, and endogenous hormone levels. Results reveal that OBZ significantly inhibited tobacco growth and triggered a reactive oxygen species (ROS) burst. Additionally, OBZ disrupted antioxidant enzyme activities and hormonal balance. Exogenous Bc mitigated OBZ toxicity by adsorbing OBZ, directly scavenging ROS, and restoring the ascorbate-glutathione (AsA-GSH) cycle, thereby enhancing photosynthetic efficiency, while Si alleviated stress via cell wall silicification, preferential regulation of root development and hormonal signaling, and repair of chlorophyll biosynthesis precursor metabolism and PSII function. The mechanisms of the two stress mitigators were complementary, Bc primarily relied on physical adsorption and ROS scavenging, whereas Si emphasized metabolic regulation and structural reinforcement. These findings provide practical strategies for simultaneously mitigating organic UV filter pollution and enhancing plant resilience in contaminated soils. Full article

Soil salinization severely limits plant growth and productivity. Mulberry (Morus alba L.), an economically and ecologically important tree, is widely cultivated, yet its salt-tolerance mechanisms at the seedling stage remain insufficiently understood. This study investigated the physiological and biochemical responses of two-year-old mulberry (‘Tailai Sang’) seedlings subjected to six NaCl treatments (0, 50, 100, 150, 200, and 300 mmol L⁻¹) for 28 days. Results showed that growth parameters and photosynthetic gas exchange exhibited dose-dependent declines. The reduction in net photosynthetic rate (Pn) was attributed to both stomatal limitations (decreased stomatal conductance) and non-stomatal limitations, as evidenced by a significant decrease in the maximum quantum efficiency of photosystem II (Fv/Fm) under high salinity. To cope with osmotic stress, seedlings accumulated compatible solutes, including soluble sugars, proteins, and proline. Critically, mulberry seedlings demonstrated effective ion homeostasis by sequestering Na⁺ in the roots to maintain a high K⁺/Na⁺ ratio in leaves, a mechanism that was compromised above 150 mmol L⁻¹. Concurrently, indicators of oxidative stress—malondialdehyde (MDA) and H₂O₂—rose significantly with salinity, inducing the activities of antioxidant enzymes (SOD, CAT, APX, and GR), which peaked at 150 mmol L⁻¹ before declining under extreme stress. A biomass-based LC₅₀ of 179 mmol L⁻¹ NaCl was determined. These findings elucidate that mulberry salt tolerance is a coordinated process involving three key mechanisms: osmotic adjustment, selective ion distribution, and a robust antioxidant defense system. This study establishes an indicative tolerance threshold under controlled conditions and provides a physiological basis for further field-based evaluations of ‘Tailai Sang’ mulberry for cultivation on saline soils. Full article

Background: Developments in biology, genetics, soil science, plant breeding, engineering, and agricultural microbiology are driving advances in soil microbiology and microbial biotechnology. Material and methods: The literature for this review was collected by searching leading scientific databases such as Embase, Medline/PubMed, Scopus, and Web of Science. Results: Recent advances in soil microbiology and biotechnology are discussed, emphasizing the role of microorganisms in sustainable agriculture. It has been shown that soil and plant microbiomes significantly contribute to improving soil fertility and plant and soil health. Microbes promote plant growth through various mechanisms, including potassium, phosphorus, and zinc solubilization, biological nitrogen fixation, production of ammonia, HCN, siderophores, and other secondary metabolites with antagonistic effects. The diversity of microbiomes related to crops, plant protection, and the environment is analyzed, as well as their role in improving food quality, especially under stress conditions. Particular attention was paid to the diversity of microbiomes and their mechanisms supporting plant growth and soil fertility. Conclusions: The key role of soil microorganisms in sustainable agriculture was highlighted. They can support the production of natural substances used as plant protection products, as well as biopesticides, bioregulators, or biofertilizers. Microbial biotechnology also offers potential in the production of sustainable chemicals, such as biofuels or biodegradable plastics (PHA) from plant sugars, and in the production of pharmaceuticals, including antibiotics, hormones, or enzymes. Full article

Aluminum (Al) stress is an important factor that inhibits crop growth in acidic soils and poses a threat to pumpkin (Cucurbita moschata) production. In this study, we investigated the effect of endophyte (endophyte) strain J01 of blueberry (Vaccinium uliginosum) on the growth, development, and transcriptional regulatory mechanisms of pumpkin under aluminum stress. The results showed that the blueberry endophyte strain J01 significantly increased the root length of pumpkin under aluminum stress, promoted the growth of lateral roots, and increased root vigor; strain J01 reduced the content of MDA and the relative conductivity in the root system; strain J01 enhanced the activities of superoxide dismutase and catalase in the root system but inhibited ascorbate peroxidase activity. Transcriptome analysis further revealed that strain J01 significantly regulated the expression of key genes associated with aluminum tolerance, including the upregulation of transporter protein genes (aluminum-activated malate transporter and aquaporin), affecting the gene expression levels of genes encoding antioxidant enzymes (ascorbate peroxidase and glutathione S-transferase) and cell wall modification genes (xyloglucan endotransglucosylase/hydrolase and pectin methylesterase). This study provides a theoretical basis and practical guidance for using microbial resources to improve aluminum tolerance in cucurbit crops. Full article

Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant physiology and soil function through diverse molecular mechanisms. PGPB synthesizes indole-3-acetic acid (IAA) to stimulate root development and nutrient uptake and produce ACC deaminase, which lowers ethylene accumulation under stress, mitigating growth inhibition. They also enhance nutrient availability by releasing phosphate-solubilizing enzymes and siderophores that improve iron acquisition. In parallel, PGPB activates jasmonate and salicylate pathways, priming a systemic resistance to biotic and abiotic stress. Through quorum sensing, biofilm formation, and biosynthetic gene clusters encoding antibiotics, lipopeptides, and VOCs, PGPB strengthen rhizosphere colonization and suppress pathogens. These interactions contribute to microbial community recovery, an improved soil structure, and enhanced nutrient cycling. This review synthesizes current evidence on the molecular and physiological mechanisms by which PGPB enhance soil restoration in degraded agroecosystems, highlighting their role beyond biofertilization as key agents in ecological rehabilitation. It examines advances in nutrient mobilization, stress mitigation, and signaling pathways, based on the literature retrieved from major scientific databases, focusing on studies published in the last decade. Full article

Soil salinization poses a significant constraint to agricultural productivity. However, certain plant growth-promoting bacteria (PGPB) can mitigate salinity stress and enhance crop performance. In this study, a bacterial isolate, R-18, isolated from saline-alkali soil in Ningxia, China, was identified as Enterobacter bugandensis based on 16S rRNA gene sequencing. The isolate was characterized for its morphological, biochemical, and plant growth-promoting traits and was evaluated for its potential to alleviate NaCl-induced stress in maize (Zea mays L.) under hydroponic conditions. Isolate R-18 exhibited halotolerance, surviving at NaCl concentrations ranging from 2.0% to 10.0%, and alkaliphilic adaptation, growing at pH 8.0–11.0. Biochemical assays confirmed it as a Gram-negative bacterium, displaying positive reactions in the Voges–Proskauer (V–P) tests, catalase activity, citrate utilization, fluorescent pigment production, starch hydrolysis, gelatin liquefaction, and ammonia production, while testing negative for the methyl red and cellulose hydrolysis. Notably, isolate R-18 demonstrated multiple plant growth-promoting attributes, including nitrogen fixation, phosphate and potassium solubilization, ACC deaminase activity, and indole-3-acetic acid (IAA) biosynthesis. Under 100 mM NaCl stress, inoculation with isolate R-18 significantly enhanced maize growth, increasing plant height, stem dry weight, root fresh weight, and root dry weight by 20.64%, 47.06%, 34.52%, and 31.25%, respectively. Furthermore, isolate R-18 improved ion homeostasis by elevating the K⁺/Na⁺ ratio in maize tissues. Physiological analyses revealed increased chlorophyll and proline content, alongside reduced malondialdehyde (MDA) levels, indicating mitigated oxidative damage. Antioxidant enzyme activity was modulated, with decreased superoxide dismutase (SOD) and peroxidase (POD) activities but increased catalase (CAT) activity. These findings demonstrated that Enterobacter bugandensis R-18 effectively alleviated NaCl-induced growth inhibition in maize by enhancing osmotic adjustment, reducing oxidative stress, and improving ion balance. Full article

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization. Full article

Fungal communities in high plateau ecosystems remain understudied despite their crucial roles in soil ecosystems, and yeasts inhabiting extreme regions have potential for industrial and biotechnological applications. We studied the fungal diversity in soils across 14 Chilean Altiplano sites using amplicon-based metagenomics and isolation of yeasts to assess their growth under various conditions and hydrolytic enzyme secretion. Using the metagenomic approach, the Ascomycota and Basidiomycota phyla were found to be the most abundant (85% and 8%, respectively). Unclassified families and genera prevailed at six and ten sites, respectively. At the other sites, the most abundant families included Cladosporiaceae, Teratosphaeriaceae, and Sporormiaceae, and the genera Oleoguttula, Coniochaeta, and Peziza. Biodiversity indices did not correlate with the soil’s geographic origin, organic matter content, humidity, or pH. Most isolated yeasts belong to the Naganishia, Holtermanniella, and Vishniacozyma genera, growing at temperatures ranging from 4 °C to 26 °C. Most isolates could use glucose, sucrose, and maltose as carbon sources and exhibited amylase, esterase, pectinase, and protease activities at 30 °C and below. Our results indicate that the evaluated soil physicochemical parameters do not explain the fungal distribution in the Altiplano and highlight the region as a reservoir of unknown fungi, including yeasts with industrially relevant enzymes. Full article

Cordyceps takaomontana is a medicinal fungus with significant pharmacological value, but how soil microbes promote its growth remains unclear. We established a solid-state co-culture system involving C. takaomontana synnemata and its native soil fungi of Fusarium paeoniae and Bjerkandera minispora. Both F. paeoniae and B. minispora significantly promoted synnematal growth and enhanced antioxidant enzyme activities. Total triterpenoid content increased substantially. F. paeoniae markedly elevated levels of ergosterol peroxide, whereas B. minispora boosted accumulation of L-arabinose, ergotamine, and euphol. Metabolomics revealed that both fungi activated key metabolic pathways (including ABC transporters, mineral absorption, and protein digestion/absorption). F. paeoniae uniquely upregulated phenylalanine metabolism. This work elucidates the metabolic mechanisms underlying growth promotion of C. takaomontana mediated by F. paeoniae and B. minispora as well as deciphers potential pharmacologically active metabolites. These findings provide a foundation for strategically improving artificial cultivation and developing functional microbial inoculants. Full article