Search Results (363)

Background/Objectives: Municipal wastewater treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria, which pose a threat to global public health. In this study, we used whole-genome sequencing (WGS) to characterize antibiotic resistance genes (ARGs) and their association with mobile genetic elements (MGEs) in five multidrug-resistant (MDR) Escherichia coli isolates from dewatered sludge cake samples collected from a municipal WWTP in Cheongju, Republic of Korea. Methods: Susceptibility to nine antibiotics was evaluated via disk diffusion assay. Among the isolates exhibiting multidrug resistance (MDR) to three or more antibiotic classes, five isolates were randomly selected for whole-genome sequencing using the Illumina NovaSeqX platform. Additionally, we compared the genomic structures of five WWTP isolates with 35 environmental E. coli isolates from South Korea deposited in the NCBI pathogen database. ARGs and MGEs, including plasmids, integrons, and insertion sequences (ISs), were detected in the genome assemblies. Results: ARGs were differentially distributed between chromosomal and plasmid-derived contigs. Efflux pump-related genes were predominantly located on the chromosome across all isolates, whereas several beta-lactamase genes (e.g., bla_TEM-30 and bla_TEM-33), fluoroquinolone, and tetracycline resistance genes were localized on putative plasmid contigs. Furthermore, we characterized specific MGEs associated with these ARGs, including a class 1 integron gene cassette (dfrA17–aadA5–qacEΔ1–sul1) and an IS-mediated module (mph(A)–mrx–IS6100). Core-genome multilocus sequence typing (cgMLST) revealed that these MDR isolates represented diverse genetic lineages rather than a single clonal cluster. Conclusions: The results from this study highlight the necessity of enhanced post-treatment management of wastewater byproducts and WGS-based surveillance to mitigate the environmental spread of MDR bacteria. Full article

Plant growth-promoting rhizobacteria (PGPR) are considered promising bio-inoculants for poplar production, but their effects can vary depending on bacterial strain, host genotype, and growth environment. In this study, we evaluated the responses of ten poplar clones representing three taxonomic groups to five indigenous PGPR strains under greenhouse and open-field nursery conditions. Under greenhouse conditions, Priestia aryabhattai GJRr2, Variovorax boronicumulans HNRr1, and a mixed inoculum (Mix) showed the most consistent positive effects. Plant height increased from 86.1 ± 5.6 cm in the control to 156.0 ± 9.4 cm in the GJRr2 treatment, whereas HNRr1 produced the greatest stem diameter (9.01 ± 0.26 mm) and total fresh weight (94.0 ± 6.0 g). Clone identity explained a larger independent fraction of growth variation than bacterial strain, and the strongest integrated responses were observed in I-476, Dorskamp, and Eco28. Field responses were generally weaker, but GJRr2 and Mix still increased height, DBH, and stem volume, whereas ORa was associated with negative responses in these traits. These results demonstrate that PGPR effects in poplar are strain-specific, clone-dependent, and environmentally contingent, indicating that inoculant selection should account for both host genotype and performance stability across growth conditions. Full article

Light availability is a key environmental factor influencing plant functional traits and ecological strategies. To investigate how natural populations of Iris pumila respond to contrasting irradiance, we conducted an in situ reciprocal transplant experiment using clonal genotypes from two natural populations, each originating from an open dune and a shaded forest habitat. Leaves collected from each of the replanted and transplanted genotypes were analyzed for structural (specific leaf area—SLA, leaf dry matter content—LDMC), physiological (specific leaf water content—SLWC, photosynthetic pigments) and biochemical (peroxidase—POD, glutathione reductase—GR, phenolics and anthocyanins) traits. Shade-grown individuals developed thinner leaves with higher SLA and chlorophyll content, enhancing light-harvesting efficiency, whereas sun-exposed plants exhibited greater LDMC, increased POD and GR activities and higher anthocyanin levels—traits consistent with enhanced photoprotection under high irradiance. All genotypes exhibited pronounced plasticity to light intensity, with habitat exerting a stronger influence on trait expression than population origin. To evaluate oxidative balance, we proposed the ODAC index (Oxidative Damage to Antioxidant Capacity), which integrates lipid peroxidation with antioxidant capacity. ODAC values revealed consistent population-level differences, with higher values in Dune genotypes across habitats, indicating a constitutively elevated oxidative load relative to antioxidant protection and suggesting differentiation in redox regulation between populations. Overall, leaf trait variation in I. pumila appears to be primarily driven by plastic responses to light conditions, while differentiation in oxidative physiology contributes to functional divergence between populations. Full article

Clonal propagation of rust-resistant sugar pine (Pinus lambertiana Dougl.) is currently limited by extreme rooting recalcitrance and highly variable donor responses to nursery management. This study identified seed zone-specific nutritional sensitivities and evaluated rooting success; we hypothesized that northern seed sources would exhibit greater sensitivity to high nutrient loads and that stable microclimates would outperform high-intensity rooting systems. In Study 1, seedlings from five United States Department of Agriculture seed zones were grown for 27 weeks in five nutrient solutions (tap-water control, modified Hoagland, Foliage-Pro^®, Andrejow, and FloraNova^®) spanning 0.72–3.00 dS m⁻¹. The nutrient-rich Foliage-Pro^® and FloraNova^® solutions defined the upper end of the nutrient-intensity range and revealed strong seed zone contrasts: northern zones (526, 550) showed marked sensitivity, with survival declining from 70 to 100% in the control to 15–40% under the highest-EC formulations, whereas southern zones (992, 993) maintained high survival (≥75%) across all treatments and exhibited increased branching (up to 3.7 branches plant⁻¹) under higher-nutrient solutions. In Study 2, stem cuttings were rooted in three environments (non-mist, hydroponic, and aeroponic) and four hormone treatments (control, Clonex^®, Dip’n Grow^®, and IBA + Ethrel). Rooting occurred exclusively in the non-mist propagator; untreated controls achieved 65% success and outperformed all hormone treatments (0–10%). These results demonstrate that P. lambertiana propagation depends on seed zone-specific donor nutrition and stable, hormone-independent rooting environments. Full article

Ulluco (Ullucus tuberosus Caldas) is an Andean tuber crop of high nutritional and genetic importance. However, its vegetative propagation promotes the accumulation of pathogens and limits the availability of uniform, high-quality planting material. In this study, an efficient and reproducible in vitro micropropagation protocol was established for an ulluco genotype from the Amazonas region of Peru. Nodal segments were cultured on MS (Murashige and Skoog) medium supplemented with 6-benzylaminopurine (BAP) or kinetin (KIN) at increasing concentrations (0.0–2.0 mg L⁻¹). For rooting, in vitro-derived shoots were transferred to MS medium supplemented with indole-3-butyric acid (IBA) or 1-naphthaleneacetic acid (NAA) at the same concentration range (0.0–2.0 mg L⁻¹). The explants exhibited a high basal morphogenetic capacity; however, the addition of cytokinins significantly enhanced the response. KIN at 2.0 mg L⁻¹ achieved 100% regeneration, whereas BAP at 0.2 mg L⁻¹ maximized shoot proliferation, producing 2.07 shoots per explant. Shoot elongation was greater with KIN at 1.0 mg L⁻¹, reaching 39.15 mm. In the rooting phase, the response varied depending on the type and concentration of auxin. NAA at 0.1 mg L⁻¹ resulted in 100% rooting and produced the greatest root length (41.93 mm), whereas IBA at 0.1 mg L⁻¹ maximized the number of roots (4.67), although roots were shorter. Rooted plantlets exhibited 100% survival after eight weeks of acclimatization. This protocol provides an effective system for the rapid production of vigorous and uniform clonal plants and represents a useful tool for the propagation, conservation, and future biotechnological improvement of ulluco. Full article

Papaya (Carica papaya L.) is a highly cross-pollinated crop that exhibits considerable genetic variability when propagated through seeds, resulting in non-true-to-type progeny. Therefore, the development of an efficient in vitro regeneration system is essential for large-scale clonal propagation of elite cultivars. In the present study, a highly efficient and reproducible somatic embryogenesis protocol was developed for C. papaya var. TNAU Papaya CO 8 using immature zygotic embryos as explants. This study provides the first comprehensive comparative evaluation of three basal media, viz., Murashige and Skoog Medium, N6 Medium, and Woody Plant Medium, for somatic embryogenesis and plant regeneration in this variety, along with the optimization of polyamine-enriched media for enhanced plantlet recovery. The embryogenic potential of explants was assessed across different stages, including callus induction, somatic embryo development, plant regeneration, shoot elongation, rooting, and acclimatization. Maximum callus induction (81.96%) was observed on half-strength MS medium supplemented with 2,4-Dichlorophenoxyacetic acid under dark conditions, followed by ½ N6 (63.00%) and ½ WPM (58.02%). Somatic embryo initiation was highest on ½ MS medium containing 2.0 mgL⁻¹ 2,4-D (77.82%). Somatic embryos developed through distinct globular, heart, torpedo, and cotyledonary stages. Embryo maturation was significantly enhanced on MS medium supplemented with abscisic acid, polyethylene glycol, benzylaminopurine, and proline. The highest plantlet regeneration (85.02%) was achieved on MS medium enriched with putrescine, whereas comparatively lower regeneration was recorded on N6 (75.99%) and WPM (57.97%). Shoot elongation was significantly improved by supplementation with gibberellic acid (1.0 mgL⁻¹). Root induction was optimal on half-strength MS medium containing Indole-3-butyric acid, 1-Naphthaleneacetic acid, phloroglucinol, and activated charcoal, resulting in well-developed roots. Regenerated plantlets were successfully acclimatized in a cocopeat–vermicompost substrate with a survival rate of 74.01%. The optimized protocol provides a reliable and efficient system for large-scale clonal propagation and offers promising applications in genetic transformation and commercial production of papaya var. TNAU papaya CO 8. Full article

Artemisia maritima holds potential applications in the rehabilitation of degraded environments, particularly in salt-affected areas, for biosaline agriculture aimed at biomass production for further valorization and green biotechnology. The aim of the present study was to investigate the response of A. maritima to alterations in soil chemical composition, including differences in mineral supply, the addition of various sodium salts, and contamination with several heavy metals (cadmium, lead, copper, manganese, zinc), in order to establish a scientific basis for further applied research. Under standard fertilization conditions, the growth of A. maritima plants was restrained by nitrogen deficiency. Surplus nitrogen enhanced mineral uptake and growth, especially for shoots, and stimulated clonal development. Low to moderate (50 and 100 mmol L⁻¹) NaNO₃ treatment significantly stimulated shoot growth, while Na₂HPO₄ and NaHCO₃ treatments exhibited the most adverse effects at 200 and 400 mmol L⁻¹, resulting in reduced growth and biomass, and even the deterioration of the aboveground parts. Chlorophyll fluorescence parameters served as reliable early indicators of the detrimental effects of salinity associated with individual anions. Shoot macronutrient levels remained unchanged for phosphorus and calcium, while nitrogen increased in nitrate treatments. Root mineral nutrient content was more susceptible to salinity, with significant changes observed for all macro- and micronutrients, varying depending on the specific element and anion type. The alterations in mineral nutrition observed for each anion treatment exhibited distinct characteristics. A. maritima plants demonstrated high tolerance to all heavy metals, with roots being more susceptible compared to shoots. At the shoot level, statistically significant growth inhibition was evident only for 1000 mg L⁻¹ lead and 1000 mg L⁻¹ zinc treatments. A. maritima plants can be characterized as high accumulators of cadmium, lead, manganese, and zinc, and as extreme accumulators of copper in shoots. Nitrophily, clonal expansion with a help of bud-bearing roots, and the ability to accumulate relatively high concentrations of mineral elements in shoots are among the important physiological characteristics of A. maritima plants, enabling them to exhibit high resilience in environmentally heterogeneous habitats. Full article

Intraspecific phenotypic diversity in clonally propagated crops is frequently constrained by narrow domestication histories and the widespread use of a limited number of elite cultivars. In Stevia rebaudiana, commercial production has largely centred on cv. ‘Morita II’, raising concerns about reduced diversity and adaptive potential. This study characterised and structured phenotypic diversity within a segregating population derived from ‘Morita II’ under tropical field conditions. Eighty-six progeny-derived genotypes (clonally propagated) plus the commercial control (87 genotypes total) were evaluated using 25 agromorphological descriptors (qualitative and quantitative). Quantitative traits showed broad variation, including plant height (28.26–119.50 cm) and dry yield rate (0.94–28.55 g plant⁻¹). Multivariate analyses of mixed descriptors (PCA and hierarchical clustering based on Gower distance) identified plant architecture, vegetative growth, and phenology as the main sources of differentiation. The first two principal components explained 19.65% and 12.58% of total phenotypic variance, respectively (32.23% cumulative). Hierarchical clustering (UPGMA; dissimilarity cut-off = 0.25) resolved four phenotypic groups (GI–GIV) with sizes n = 3, 1, 66, and 17, respectively, enabling the definition of contrasting ideotype candidates based on recurrent trait combinations. These results provide a quantitative baseline for phenotypic structuring, prioritization of materials for further evaluation, and management of clonal stevia collections in tropical production systems. These ideotype candidates should be considered preliminary until validated across environments and linked to chemical quality traits. Full article

Walnut (Juglans regia L.) performance and sustainability are closely linked to soil–plant–microbe interactions; nowadays, the combined influence of edaphic context, plantation development and rootstock genotype on walnut-associated microbiomes remains insufficiently resolved. Here, we integrated soil physicochemical characterization, community-level physiological profiling and 16S rRNA gene amplicon sequencing across walnut plantations in four Spanish regions. The design included 14-year clonal stands (Galicia, Gerona, Toledo), an age gradient in Galicia (4, 9 and 14 years), and four rootstocks (MJ209, Vlach, own-rooted ‘Chandler’ and J. regia seedling) in the Córdoba plantation. At the community-level, rhizospheres exhibited higher overall metabolic activity, displaying substrate-specific functional fingerprints across regions. Regarding stand ages, a functional peak was observed at middle age, with a decline in richness and diversity with age. Moreover, rootstock genotype further modulated rhizosphere metabolic function. Sequencing supported compositional differences among regions, ages and rootstocks, identifying a bacterial core of Juglans spp. rhizosphere and detecting 36 putative Plant Growth-Promoting Rhizobacteria (PGPR) genera, suggesting a potential reservoir and possible uses in plant biotechnology. Overall, walnut-associated microbiomes are jointly structured by soil gradients, plantation development and rootstock genotype, supporting site and genotype-tailored microbiome management. Full article

Phosphorus (P) deficiency in forest soils is a key constraint on the sustainable management and productivity of Chinese fir (Cunninghamia lanceolata) plantations. This study investigated how P limitation alters the reciprocal exchange of “photosynthetic carbon and mineral phosphorus” between Chinese fir and arbuscular mycorrhizal fungi (AMF) when the focal plant grows adjacent to neighbors with different degrees of relatedness. An indoor pot experiment simulating heterogeneous P supply was conducted using clonal seedlings of Chinese fir No. 36 as the focal plant, with Chinese fir No. 36, Chinese fir No. 41, and Schima superba as neighboring plants to establish three two-plant combinations: a kin pair (No. 36 + No. 36), a close-kin pair (No. 36 + No. 41), and an unrelated-kin pair (No. 36 + S. superba). Funneliformis mosseae was inoculated into the shared root-zone room connecting the two plants, and the neighbor was subjected to a gradient of P limitation (sufficient P, low P, and zero P). Meanwhile, the focal No. 36 plant received ¹³CO₂ pulse labeling to form a “Chinese fir–AMF–P-limited neighbor” symbiotic network in which No. 36 served as the ¹³C donor. AMF colonization, seedling growth, and changes in ¹³C enrichment and P concentration in plant tissues of the focal plant were quantified. Neighbor P limitation significantly increased AMF colonization in roots and whole-plant P concentration of the focal Chinese fir. Following ¹³CO₂ pulse labeling, whole-plant ¹³C enrichment of the focal plant increased significantly under the neighbor zero P treatment, suggesting enhanced carbon allocation under severe neighbor P limitation. Moreover, under the neighbor zero P treatment, focal plants grown with an unrelated-kin neighbor showed significant increases in stem P concentration (1.86 g·kg⁻¹) and stem atom% ¹³C (1.50%), whereas focal plants grown with a kin neighbor exhibited a significant increase in root Atom% ¹³C (1.29%). These patterns indicate that neighbor relatedness may modulate carbon allocation and P acquisition within the mycorrhizal network: in the kin context, the focal plant tended to allocate more photosynthetic carbon belowground and may partially subsidize the AMF carbon demand (i.e., a higher C reward), coinciding with a relatively weaker P accumulation in its own tissues; in contrast, in the unrelated kin context, carbon allocation shifted toward stems and was associated with strengthened P accumulation in stem tissues. Overall, the results highlight the dynamic nature of AMF-mediated carbon–nutrient reciprocity across hosts of contrasting relatedness and provide new insights into how mycorrhizal networks may facilitate plant adaptation to nutrient limitation. Full article

In response to the problems of loose soil structure and insufficient water and nutrient retention capacity of sandy bank slopes in arid regions, which constrain vegetation establishment and long-term slope stability, this study focuses on typical sandy soils in arid northwestern China. The desert plant Alhagi sparsifolia, characterized by clonal root sucker reproduction, was selected as the study species to construct and optimize a composite-amended sandy substrate suitable for ecological restoration of bank slopes. Based on an orthogonal experimental design, carboxymethyl cellulose sodium (CMC), straw fibers (SF), and fly ash (FA) were combined at different proportions to assess (i) the vertical distribution of soil water and nutrients in the A. sparsifolia growth habitat, (ii) aggregate structure, (iii) plant trait responses to environmental regulation, and (iv) the shear strength of root–soil composites. The results indicate that when the contents of CMC, SF, and FA were 0.5%, 1.0%, and 5.0%, respectively, the substrate environment promoted a vertically oriented root system with pronounced lateral root development in A. sparsifolia, and the plants adopted an adaptive strategy that balances resource acquisition efficiency and environmental constraints by regulating aboveground growth allocation. This growth pattern reduced the risk of disturbances to slope stability caused by excessive aboveground biomass while maintaining the sand-fixing function of root morphological traits. This study provides a plant functional trait-based regulation strategy for ecological restoration of typical sandy slopes in arid regions, and the proposed composite substrate optimization scheme offers a feasible reference for improving vegetation establishment and substrate performance in sandy habitats. Full article

The cacao tree (Theobroma cacao L.) is a crop of great economic importance to Brazil and has undergone several breeding processes that, among other things, have made it possible to obtain several self-compatible genotypes, ensuring that there is no genotypic variation in the crop, with the differences observed in the plants being caused only by the environment. For this to continue, the proper and reliable execution of scientific experiments is essential, and quantifying the material needed to carry out these experiments, i.e., the plot size, is an important step. This requires a scientific justification for choosing the plot size. In the literature, various plot sizes are adopted in experiments with seedlings. Therefore, the objective was to determine the optimal plot size for experiments with clonal cacao seedlings. The method adopted was the modified maximum curvature method using a bootstrap resampling simulation with 2000 replacements. The genotypes CCN10, CCN51, CP2204, CP2176, PS1319, and PH16 were evaluated based on 13 morphological characteristics and three quality indices used in morphological characterization studies of seedlings. The optimal plot size for experimentation with cocoa seedlings is nine plants per experimental plot. Full article

Lateral flow immunoassays (LFAs) are widely used for on-site testing; however, their use for the rapid detection of plant viruses in the field is often limited by inconvenient sample preparation. Here, we present a new sampling method and a simplified dipstick LFA format for the detection and monitoring of cowpea chlorotic mottle virus (CCMV) as a model plant pathogen. The assay employs a monoclonal mouse antibody for capture and a poly-clonal rabbit antibody conjugated to 80 nm gold nanoparticles for detection. Conventional sample and conjugate pads are omitted, allowing the test strips to be dipped directly into wells containing plant extract and antibody–gold conjugate. No plastic casing was required, which could lead to a reduction in waste. It was shown that CCMV concentrations as low as 3.5 µg/L or 350 pg per sample could be reliably detected in 15 min. Specificity tests confirmed that other plant viruses, cowpea mosaic virus (CPMV) and tobacco mosaic virus (TMV), did not produce false-positive results. In addition, we describe a new method for on-site sampling using a manual punch and a syringe equipped with a frit. This step combines grinding the sample, extraction, filtration, and reconstitution and mixing of the antibody-gold conjugate, enabling the analysis of punched leaf disks without laboratory equipment. When applied to CCMV-infected cowpea plants, the assay revealed systemic infection before visual symptoms became apparent. This work demonstrates that simplified LFAs combined with innovative sampling techniques can provide sensitive, specific, and rapid diagnostics for crop monitoring and support early intervention strategies in agriculture. Full article

CRISPR-Cas9 technology has opened new perspectives in genome editing of clonally, asexually propagated and polyploid plants by enabling multiple allelic gene edits. Traditional Agrobacterium- and particle bombardment-mediated transformations, which rely on integration of gene-editing transgene cassettes, have been efficiently applied to several plants; however, concerns about the acceptability of resultant edited transgenic genotypes make these methods less attractive for vegetatively propagated crops. We leveraged and optimized the CRISPR-Cas9/sgRNA-RNPs system for delivery into protoplasts of the hexaploid sweetpotato cultivar PI-318846, targeting eukaryotic translation initiation factor isoform 4E genes to enhance resistance to SPFMV potyviruses. To evaluate the efficiency of pre-assembled Cas9/sgRNA-RNP in sweetpotato transfection, single guide RNAs were designed to target putative host susceptibility genes: IbeIF4E, IbeIF(iso)4E, and IbCBP. Freshly isolated leaf protoplasts were subjected to CRISPR-CAS9-RNP PEG-mediated transfection under different parameters. Sweetpotato regenerants screened using PCR-RE-T7 assay, sequencing, and Inference CRISPR Edit analyses of target-site amplicons revealed the most efficient editing conditions utilizing 25% PEG with a 3:1 (15 µg:45 µg) ratio of Cas9/sgRNA-RNP for 25 min and 48 h incubation period. Different allelic InDels were obtained with editing efficiencies of 10–20% in regenerated plantlets, demonstrating that PEG-mediated CRISPR-RNP transfection system is key for advancing DNA-free editing tools in polyploid and vegetatively propagated crops. Full article

Extended-spectrum β-lactamase-producing E. coli (ESBL-EC) threatens public health by driving widespread antimicrobial resistance transmission in environmental and agricultural settings. This study examined the prevalence, genetic determinants, and phylogenetic relationships of ESBL-EC isolated from municipal wastewater treatment plants (WWTPs) and farm environments in southeastern North Carolina. A cross-sectional survey was conducted between May and September 2025 across two WWTPs and two farms (cattle and poultry). We sampled influent and effluent wastewater, plus fecal and water specimens collected from chickens, ducks, and cattle. Antimicrobial susceptibility testing was performed using the Kirby–Bauer disk diffusion method against nine drugs, while PCR and sequencing were used for genotypic characterization. Phylogenetic analysis assessed genetic relatedness among isolates. ESBL-EC was detected in 27.4% (n = 124) of 452 samples, with the highest prevalence in chickens (31.5%), followed by WWTP influents (28.2%), ducks (18.5%), and cattle (12.1%). Dominant resistance genes included blaCMY-2 (71.8%), blaCTX-M-1 and blaOXA (54% each), and blaSHV (29.8%). Co-occurrence of blaCMY-2 with blaCTX-M-1 and blaOXA was observed in poultry isolates. Phylogenetic analysis revealed clonal relatedness between poultry and cattle isolates. These findings highlight poultry as a key reservoir and emphasize the need for One Health surveillance to mitigate cross-reservoir transmission of resistant E. coli. Full article