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Background/Objectives: Certain strains of Lactobacillus acidophilus are widely used as probiotics. However, their functional potential for female reproductive tract health remains insufficiently characterized. While most studies have focused on individual strains, the distribution of putative probiotic-associated genes across the species remains unclear. This study aimed to evaluate the vaginal probiotic potential of Lb. acidophilus using population genomic analysis and comparative phenotypic characterization. Methods: Pan-genomic analysis was performed on 109 Lb. acidophilus genomes (107 public genomes and 2 vaginal isolates). Putative probiotic-associated gene clusters were identified by functional annotation, categorized into functional modules, and compared among ecological-origin groups. Two vaginal isolates (strains A2 and A3) were characterized in vitro for growth under different pH conditions, cell surface hydrophobicity, lactic acid and hydrogen peroxide production, antimicrobial activity, hemolysis, and antimicrobial susceptibility. Results: The Lb. acidophilus pan-genome was closed, with 1782 of 1902 gene clusters (93.69%) classified as core. Thirty-six putative probiotic-associated gene clusters were identified and grouped into four modules: environmental tolerance, adhesion/colonization, exopolysaccharide/biofilm synthesis, and nutrient metabolism/microbial competition. Thirty-four of the 36 gene clusters were present in all 109 genomes, and no general ecological origin-specific distribution pattern was observed. Three bacteriocin-related gene clusters were conserved across all genomes. A2 and A3 exhibited similar lactic acid production and growth patterns at pH 4–6. Both produced relatively low amounts of hydrogen peroxide compared with the reference strains. A3 showed higher cell surface hydrophobicity and moderate inhibition against Gardnerella vaginalis, while A2 showed no inhibition of this organism. Both isolates were non-hemolytic, and were susceptible to vancomycin and linezolid, resistant to clindamycin, and non-susceptible to daptomycin. No acquired antibiotic resistance genes were detected. Conclusions: Most putative probiotic-associated gene clusters were conserved across the Lb. acidophilus population, whereas A2 and A3 showed strain-dependent phenotypic differences. These findings support combining population genomic analysis with strain-level phenotypic testing when selecting Lb. acidophilus candidates for bacterial vaginal infections. Full article

Despite the critical role of essential nutrients in maintaining overall health in freshwater organisms, the effects of nutritional deficiency remain largely unknown. This study investigated the biological and biochemical effects of single and combined deficiencies of boron (B), magnesium (Mg), and calcium (Ca), essential nutrients for physiological functions, in Daphnia magna. Biological responses included life-history parameters (survival, growth, and reproduction), while biochemical effects comprised catalase (CAT) and glutathione S-transferase (GST) activity, as markers of oxidative stress and detoxification, respectively. B deficiency conditions significantly affected survival, growth, reproduction, and CAT activity, while Mg-deficient conditions were associated with significantly reduced survival, long-term growth, reproduction, and CAT activity. Under Ca-deficient conditions, the most severe responses were observed, including reduced survival, growth, reproduction and increased GST activity. Combined B omission with Ca or Mg also produced pronounced adverse responses compared with the corresponding single-nutrient deficiency conditions. Fluorescence imaging revealed treatment-dependent differences in B-associated fluorescence, consistent with differences in B availability. Impaired life-history traits and elevated GST activity suggest cellular stress or activation of detoxification processes associated with reduced organismal performance. The findings demonstrate that nutrient deficiencies act as chronic stressors, highlighting the ecological importance of essential nutrient scarcity in freshwater ecosystems. Full article

Crop rotation and fertilization are two of the most important agrotechnical measures that influence the chemical properties of the soil and its capacity to support stable agricultural production, especially in areas affected by erosion and climate change. The aim of this study was to evaluate the influence of crop rotation and fertilization on the main soil properties (pH, total nitrogen, available phosphorus and potassium, humus content) in moderately eroded cambic chernozems of the Bârlad Plateau, as well as the effect of experimental factors on wheat yield. The research was carried out in the period 2021–2025 in a stationary experiment located on a slope with a slope of 12–13% at “Mircea Moțoc” Soil Erosion Research and Development Station (M.M.S.E.R.D.S.) Perieni. Two wheat cropping systems were analyzed, namely, monoculture and five-year rotation, in combination with five fertilization variants (N₀P₀, N₃₂P₃₂, N₉₆P₉₆, N₁₂₈P₁₂₈ kg ha⁻¹ and 50 t ha⁻¹ manure). The determinations targeted pH, total nitrogen, mobile phosphorus, mobile potassium, humus content in the 0–20 cm and 20–40 cm soil layers and yield. The results highlight the depletion in available nitrogen, phosphorus, and potassium reserves, alteration of soil reaction in monoculture, and significant improvement in N (from 0.1% to 0.19%), P (from 95.5 to 485.5 mg ha⁻¹) and K (from 188.4 to 227.5 mg ha⁻¹) soil content at the time of final sample collection in the five-year rotation. The application of manure as well as the inclusion of legumes and perennial crops in the rotation contributed to the accumulation of organic matter, to the improvement in soil reaction and to the optimization of nutrient cycling. The highest yields, significant at p ≤ 0.001, were obtained with the application of N₉₆P₉₆ 2858 kg ha⁻¹ in monoculture and 3689 kg ha⁻¹ in the five-year rotation. The study confirms that long rotations associated with organic fertilization represent an effective strategy for the conservation of agricultural soil fertility in areas vulnerable to erosion and drought. Full article

Integrated nutrient management reduces reliance on chemical fertilizers by combining organic and inorganic inputs. A field experiment was conducted under rainfed conditions in Hungary from 2022 to 2024 to evaluate organic, inorganic and biological fertilizers applied to the high-oleic sunflower hybrid ES Emeric. Seven treatments were compared, namely, an unfertilized control, potassium (K), combined organic and inorganic nitrogen (GOIM), effective microorganisms (EM-1), and the combinations K+GOIM, K+EM-1 and GOIM+EM-1. Seed oil, crude protein and moisture content were determined, together with the fatty acid profile of the oil. Growing season influenced every measured variable far more strongly than fertilization, and all treatment responses were expressed as year-by-treatment interactions. Mean oleic acid content was 69.9% in the dry season of 2022 and 85.3% in 2024, but only 28.9% in the cooler and wetter season of 2023, when linoleic acid reached 59.8%. In 2022, K and K+EM-1 gave the numerically highest oil contents, 48.7% and 48.0%, less than one percentage point above the control, while GOIM+EM-1, GOIM and K+GOIM gave significantly higher protein contents than the remaining treatments. In the same season, EM-1 and K+GOIM raised linoleic and alpha-linolenic acids and, therefore, total polyunsaturated fatty acids, whereas GOIM+EM-1 and K increased oleic acid and total monounsaturated fatty acids. Integrated fertilization can therefore be used to shift the balance between monounsaturated and polyunsaturated fatty acids in sunflower oil, but the size and direction of the shift are governed by the conditions of the growing season. Full article

Industrial fermentation relies on mechanically agitated submerged culture, in which impeller-driven mixing improves oxygen and nutrient transfer but imposes an energy penalty and a hydrodynamic shear field that stresses cells. Solid supports offer an agitation-free alternative, yet their surface is typically ill-defined and only a single polymer and a single organism have been examined. Here we treat the support material as a controllable process variable. Using an identical scaffold geometry 3D-printed by fused-deposition modeling in four thermoplastics—ABS, TPU, PLA, and PETG—we compared static cultivation of a model yeast (Saccharomyces cerevisiae) and a model lactic acid bacterium (Lactobacillus plantarum) against shaken and static controls, and related the outcomes to polymer surface wettability. For S. cerevisiae, embedding a matrix in static medium nearly doubled biomass relative to the static control and drove glucose to near-complete assimilation, raising ethanol titres ~1.7–1.8-fold to shaken-culture levels without any agitation. For L. plantarum, three of the four matrices (PLA, ABS, PETG) exceeded both the static and the aerated shaking controls in biomass (by ~15–21%) and in lactic acid production, while the elastomeric TPU behaved like the controls. Because L. plantarum is microaerophilic, these results suggest that factors other than improved aeration, including interactions at the scaffold–liquid interface, contribute to the observed enhancement. The polymer type thus emerges as a tunable parameter for scaffold-assisted cultivation, enabling fermentation without mechanical agitation while achieving performance comparable to, and in some cases greater than, that of shaken culture. The polymer type thus emerges as a tunable determinant of performance, defining an agitation-free cultivation strategy in which the interface—rather than bulk flow—is engineered to achieve, and in some cases surpass, the productivity of conventional stirred culture. Full article

The invasive golden apple snail (Pomacea canaliculata) threatens rice agroecosystems, yet its direct density-dependent effects on flooded paddy soil biogeochemistry and bacterial communities remain unclear. We established flooded soil microcosms with four snail densities (0, 2, 4, and 6 snails/box) for 20 days, without external food inputs. Soil dissolved organic carbon (DOC), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), and the activities of β-glucosidase, N-acetyl-β-D-glucosaminidase, urease, and dehydrogenase were measured, and bacterial communities were characterized by full-length 16S rRNA gene amplicon sequencing. Snail density was significantly and positively related to all three nutrient variables and all four enzyme activities. The dominant bacterial phyla and genera remained stable, and bacterial α-diversity changed little among treatments, despite a small but significant increase in Simpson diversity in the high-density treatment. PERMANOVA detected significant differences in overall bacterial community structure among density treatments, while environmental fitting identified DOC, urease, and dehydrogenase as variables significantly associated with community variation. These findings indicate that living golden apple snails can alter nutrient availability, soil biochemical activity, and bacterial community organization in flooded paddy soil, revealing a belowground pathway through which this invader may influence paddy ecosystem functioning. Full article

Fungal nitrogen metabolism is a central determinant of yeast growth, fermentative performance, and secondary metabolism in fungi associated with fermented environments. For Saccharomyces cerevisiae, the assimilation of nitrogen sources found in grape must, including ammonium, free amino acids, and peptides, has been widely characterized, establishing a consumption hierarchy in which proline is considered a non-preferential nitrogenous source. However, the regulation and hierarchy of nitrogen-source utilization in non-conventional fungi remain poorly characterized, particularly in yeasts adapted to anthropized fermentative niches. In this context, Brettanomyces bruxellensis represents a useful fungal model to study the different nitrogen sources that are used, strain-dependent physiology, and survival under nutrient-limited fermentative conditions. We hypothesized that apparent depletion of amino acid and the expression of selected amino acid permease genes are strain-dependent traits linked to the survival of B. bruxellensis. In this study, we evaluated the strain-dependent physiology and amino acid depletion patterns of two B. bruxellensis strains from wine (LAMAP2480 and LAMAP1359). In both cases, the highest apparent depletion values under the 20 amino acid condition were observed for arginine, glutamine, tryptophan and proline, indicating that these compounds contributed substantially to the organic nitrogen pool under the assayed conditions. Only LAMAP2480 isolate was able to grow in the condition without added amino acids, indicating strain and nitrogen source dependence under limited organic nitrogen availability. Transcriptional analysis of GAP1, GNP1, and TAT1 permeases showed expression patterns dependent on both the strain and the available nitrogen source. This is the first study to combine the evaluation of physiological performance, amino acid consumption, apparent nitrogen depletion derived from amino acids normalized to OD₆₀₀ (OD-AA-N depletion), and the transcriptional responses of selected amino acid permease genes. This knowledge may contribute to understanding the survival of B. bruxellensis in fermentation environments with limited nutritional resources. Full article

Soil is a complex environmental component characterized by numerous physical, chemical, and biological attributes that determine its capacity to provide ecosystem services. While composite soil health indices are traditionally derived from static literature reviews or costly expert panels, this study evaluates the potential of general-purpose large language models as a rapid, low-cost aid for AI-driven environmental decision support. We systematically evaluate the conceptual reliability and mathematical consistency of four distinct Large Language Models (LLMs): ChatGPT, Gemini, Claude, and Copilot, in executing an Analytic Hierarchy Process (AHP) matrix integrated with the SMART criteria. The evaluation prioritized seven indicators: soil organic matter (SOM), earthworm presence, aggregate stability, electrical conductivity, available nutrients, pH, and water infiltration capacity. All platforms generated mathematically consistent AHP matrices, with consistency ratios below accepted thresholds. Across ten independent runs per platform, soil organic matter received the highest mean global weight (~0.22) and earthworms the lowest (~0.08); inter-platform agreement was statistically significant (Kendall’s W = 0.75, p = 0.007), yet single-run variability reached ~50%, showing that repeated prompting is required. This approach offers a practical framework for rapid, preliminary indicator screening under resource-constrained conditions, while revealing model-specific divergences and possible training-data biases that warrant further investigation. However, our findings suggest AI-generated AHP outputs should be treated as preliminary decision-support results and should be verified through cross-platform comparison, repeated prompting, expert review, and site-specific validation. Full article

This study aimed to investigate the effects of γ-polyglutamic acid (γ-PGA) on the physicochemical properties and enzyme activities of coal gangue-based soils, focusing on how different application rates influence soil indicators and enzyme functions for ecological restoration. Soil samples with varying weathering ages were collected from a coal gangue pile, and a pot experiment was conducted with five γ-PGA treatments (0–43.2 g dissolved in 300 mL water). Soil pH, electrical conductivity, nutrient contents, aggregate composition, and enzyme activities (urease and sucrase) were measured, and redundancy analysis (RDA) was applied to evaluate the relationships between soil properties and enzyme activities. γ-PGA rapidly increased soil pH and altered conductivity trends. Its effects on organic matter, nitrogen, phosphorus, and potassium were complex and dependent on both dosage and time. Optimal γ-PGA addition enhanced organic matter and nitrogen transformation, increased potassium availability, and modified water-stable aggregate distribution. Enzyme activities were significantly affected by γ-PGA dosage, exhibiting distinct initial levels and temporal trends across soils of different weathering ages. RDA revealed clear differentiation in soil properties under different treatments, with enzyme impacts evolving over time. DFT results revealed a distinct valence-dominated ion-binding hierarchy, with trivalent cations (Al³⁺, Cr³⁺, Fe³⁺) showing the strongest affinity, followed by divalent cations and monovalent ions/oxyanions. Overall, γ-PGA markedly improves the quality of coal gangue-based soils, providing theoretical guidance and practical reference for ecological restoration and soil management strategies. Full article

Leaf senescence is a highly programmed developmental process that enables nutrient remobilization from source to sink organs in plants. Chloroplasts serve as the primary nitrogen reservoir, and the timely degradation of their constituent proteins is essential for sustaining seed fill and crop yield. For efficient nitrogen recycling, the chloroplast proteome must be dismantled in a controlled manner through coordinated proteolytic pathways that function both inside and outside the organelle. Protein abundances are progressively reduced during senescence through the balanced action of degradation and the suppression of new synthesis, depending on the plant’s carbon–nitrogen status. Malfunctioning or damaged chloroplast components are selectively eliminated. To date, three major classes of chloroplast protein degradation systems have been characterized: the cytoplasmic ubiquitin–proteasome system (UPS), vacuolar degradation pathways, and intra-chloroplast proteases. Here we provide an updated, comprehensive overview of the three chloroplast protein degradation machineries and discuss their coordinated roles in nitrogen remobilization. We also consider how these pathways might be manipulated to improve nitrogen use efficiency (NUE) and crop productivity. Full article

Microplastics (MPs) pollution caused by agricultural film residues, organic fertilizer application, sewage irrigation, and atmospheric deposition has gradually become an unignorable interference factor to the sustainable development of the rhizosphere soil and crop in farmland. However, their specific impacts on the rhizosphere and crops remain unclear. Therefore, this review focuses on the current knowledge on the response mechanisms of rhizosphere soil and crops to MP contamination. The density of MPs is generally lower than that of soil mineral particles. Their substantial accumulation in soil can significantly reduce both the bulk density (by increasing total porosity) and the particle density (by diluting the heavy solid phase with light plastic components). The introduction of MPs disrupts the normal metabolism of soil bacterial communities; a disruption directly reflected in functional genes associated with carbon cycling. MPs can interfere with the activity of key metabolic enzymes involved in fungal nutrient cycling, thereby disrupting normal energy allocation and material metabolism. Viruses can regulate the turnover and metabolism of microbial communities through lytic and lysogenic cycles, consequently influencing the carbon fate of MPs. The toxicity and underlying mechanisms of MPs on soil fauna primarily manifest in aspects such as feeding behavior, growth and development, oxidative stress, intestinal toxicity, and reproductive toxicity. The direct effects of MPs on plants include physical barriers and mechanical damage, induction of oxidative stress, interference with nutrient uptake, disruption of photosynthesis and carbon metabolism, and disruption of plant hormone networks. This review identifies critical knowledge gaps, particularly regarding crop quality, field-based soil faunal studies, virus-microbe interactions, and degradation products, and proposes future research directions to better understand the risks MPs pose to agricultural sustainability and food safety. Full article

Assessing the soil quality of coastal reclamation areas is fundamental to alleviating land resource scarcity in coastal cities and ensuring food security. However, it remains unclear how to evaluate soil quality in reclaimed areas and identify factors driving its variation. In this study, paddy soils from four typical reclaimed coastal areas in China (Yueqing, YQ; Longgang, LG; Rui’an, RA; Longwan, LW) were investigated to construct a minimum data set via principal component analysis and to calculate soil quality indices (SQIs). YQ had higher contents of soil organic carbon (SOC: 22.82 g kg⁻¹), total nitrogen (TN: 0.14 g kg⁻¹), total water-soluble salts (TWS: 3.09 g kg⁻¹), cation exchange capacity (CEC: 21.77 cmol(+) kg⁻¹), and available Fe (44.23 mg kg⁻¹), Mn (36.63 mg kg⁻¹), Cu (30.31 mg kg⁻¹), and Zn (8.79 mg kg⁻¹) than the other sites. RA exhibited significantly higher activities of β-glucosidase (BG: 32.79 nmol g⁻¹ h⁻¹), xylanase (XYL: 5.88 nmol g⁻¹ h⁻¹), N-acetyl-β-D-glucosaminidase (NAG: 18.00 nmol g⁻¹ h⁻¹), leucine aminopeptidase (LAP: 27.01 nmol g⁻¹ h⁻¹), and acid phosphatase (PHOS: 54.50 nmol g⁻¹ h⁻¹) than the other sites (p < 0.05). LW had the greatest bacterial and fungal abundances, whereas LW displayed the highest fungal diversity. RA showed the highest SQI (SQIw: 0.49; SQIa: 0.48), followed by LW (SQIw: 0.47; SQIa: 0.47), LG (SQIw: 0.43; SQIa: 0.41), and YQ (SQIw: 0.38; SQIa: 0.41). Random forest analysis indicated that soil enzyme activities (XYL, NAG, BG, CB, PHOS), nutrients (TN, SOC, AN), fungal abundance and diversity, and TWS were key SQI predictors (Welch ANOVA p = 0.016), with XYL being the strongest predictor (p < 0.05). Collectively, soil quality in coastal reclamation areas is co-regulated by microbial metabolic activity, nutrients, and salinity, with soil enzyme activity serving as an important indicator for its assessment, thereby deepening the understanding of soil quality dynamics within these areas and enabling their sustainable management. However, the microbial mechanisms underlying these patterns across broader environmental gradients remain to be explored. Full article

To explore the effects of legume intercropping on soil nitrogen (N) and phosphorus (P) cycling processes in mulberry plantations during the winter fallow period, three treatments were set up: control (no intercropping, CK), single-legume intercropping (T1: Medicago polymorpha), and mixed-legume intercropping (T2: Medicago polymorpha + Astragalus sinicus). The variations in soil available nutrients, enzyme activities, microbial community structure, and functional gene abundances were investigated, with a focus on the influence of spatial heterogeneity (middle of inter-row as position A, and mulberry-adjacent as position B). Compared with CK, both T1 and T2 significantly altered soil microbial community composition and enhanced β-diversity (R² = 0.747, p < 0.001), and these effects were more pronounced at position A. For soil N cycling, T1 and T2 reduced available N content especially at position B; however, T2 significantly increased urease activity, while T1 decreased urease activity at position A. Both treatments elevated the abundances of N-cycling functional genes (e.g., glnA, ureC, nifD) and symbiotic nitrogen-fixing rhizobia, with T1 increasing Bradyrhizobium and T2 increasing Sinorhizobium. For soil P cycling, T1 and T2 enhanced phosphatase activity to promote organic P conversion; T1 strengthened the entire P metabolic chain by upregulating multiple P-related functional genes, while T2 specifically increased the abundance of the organic P transport gene ugpb. Structural equation modeling showed that soil microbial Shannon diversity promoted the relative abundances of N-cycling and P-cycling functional genes, and cascading pathways among nutrient-cycling genes and enzyme activities governed soil available N and P. The distinct effects of T1 and T2 highlight the importance of optimizing intercropping patterns, and spatial heterogeneity should be considered in agronomic effect evaluation. Leguminous green manure intercropping should be encouraged in mulberry plantations to boost soil nutrient-cycling processes driven by microorganisms. Full article

Background: Manure-amended agricultural soil is a critical reservoir of antibiotic resistance genes (ARGs), posing escalating threats to environmental health and food safety. However, the temporal trajectories of ARG prevalence throughout the complete reproductive cycle of cash crops, and their mechanistic linkages with fertilization regimes and microbial community succession, remain inadequately understood. Methods: To bridge this knowledge gap, we conducted an in situ field experiment over the entire growth period of Chinese cabbage at a long-term manure-amended farm in Tianjin, China. Six contrasting fertilization strategies were evaluated: unfertilized control (CK1), unfertilized baseline control (CK2), traditional full-rate combined manure–chemical fertilization (TF), traditional half-rate combined manure–chemical fertilization (T1), half-dose sole manure fertilizer (T2), and half-dose sole chemical fertilizer only (T3). Results: Our results demonstrated that ARG abundance and associated mobile genetic elements (MGEs) exhibited a pronounced transient surge immediately post-fertilization, yet reverted to baseline levels by harvest, revealing a tangible resilience of the soil resistome. Notably, the optimized half-organic fertilization (T2) effectively curtailed the proliferation of manure-derived pathogenic taxa while preserving beneficial keystone phyla (e.g., Acidobacteria and Proteobacteria), indicating a trade-off between nutrient provisioning and ecological filtering. Co-occurrence network analysis further identified MB-A2-108, Saccharimonadales, and Rokubacteriales as pivotal hosts for multidrug-resistant ARGs, underscoring that microbial interspecific interactions—rather than taxonomic richness alone—are the primary drivers of resistome succession. Quantitative risk assessment confirmed that the T2 regimen reduced the composite ARG contamination index (CF_zone) by 25% relative to conventional full fertilization (TF), while maintaining comparable cabbage yields. Conclusions: Collectively, our findings advocate for precision organic fertilization as a nature-based solution that synchronizes nutrient supply with crop demand, curtails ARG propagation, and mitigates long-term agroecological risks. Full article

Bauxite mining causes severe soil degradation in the ecologically fragile karst region of Southwest China, yet targeted vegetation restoration schemes remain poorly developed. This study aimed to screen promising selected restoration species and preliminarily explore their soil improvement characteristics in karst bauxite mine wastelands through a field observational survey. We investigated six vegetation-soil conditions at 0–10 cm topsoil (two-year monocultures of Robinia pseudoacacia, Ligustrum lucidum, Zea mays, Miscanthus sinensis, topsoil from >15-year Z. mays with straw return, and unvegetated bare land), alongside paired 10–20 cm subsoil from the same long-term Z. mays stand as a depth-profile reference, and analyzed soil physicochemical properties, enzyme activities, and bacterial/fungal communities via high-throughput sequencing. Results showed that vegetation cover neutralized strongly acidic mine soil and significantly increased soil organic matter (SOM), total nitrogen (TN), and available nutrients compared with the bare control (p < 0.05). The long-term Z. mays cropland showed the strongest soil nutrient accumulation, with topsoil SOM, available phosphorus, and available potassium, increased by 428.6%, 250.0%, and 65.3%, respectively, relative to the bare control. Notably, the subsoil of long-term Z. mays also maintained high nutrient levels, but its absolute values are not directly comparable with topsoil treatments due to different sampling depths. All vegetation conditions elevated soil enzyme activities and microbial alpha diversity and significantly shifted bacterial and fungal community structure (beta diversity) compared with the control. Several bacterial phyla (including Chloroflexi and Proteobacteria) that have been associated with carbon-cycling functions in prior studies were relatively more abundant in revegetated soils; however, their functional roles in this system remain to be verified. Redundancy analysis identified SOM, TN, and available potassium as key environmental correlates of bacterial community variation. Overall, the long-term crop–straw return pattern shows comprehensive soil improvement effects, providing observational baseline data and reference for ecological restoration of karst bauxite mining areas in Southwest China. Full article