Search Results (584)

Globally, large quantities of animal waste and human sewage sludge are generated annually. Their application as soil amendments can enhance soil quality and support a circular economy. However, these wastes may harbour pathogenic bacteria, posing contamination risks to soil and water and potential transmission to animals and humans. This study investigated the survival of five bacterial pathogens during six months of storage in five types of organic waste and following their subsequent application to soil. During storage, T₉₀ values ranged as follows: Salmonella Typhimurium (2.3–17.7 days), Campylobacter jejuni (0 to 23.9 days), Escherichia coli O157:H7 (4.3 to 57.8 days), and Listeria monocytogenes (1.9 to 170.4 days). In soil, T₉₀ values were S. Typhimurium (4.2 to 17.4 days), C. jejuni (4.8 to 26.8 days), E. coli O157:H7 (4.3 to 52.9 days), and L. monocytogenes (2 to 83.7 days). Clostridium sporogenes remained stable throughout both experiments, preventing T₉₀ calculation. Contrary to our initial hypothesis that soil microbiota would accelerate pathogen decline, T₉₀ values were higher during storage in 11 cases and higher in soil in nine scenarios. These findings highlight the need for pre-treatment strategies for animal waste and biosolids before land spreading to consistently mitigate risks of pathogen transmission and environmental contamination. Full article

The increasing contamination of agricultural soils with microplastics (MPs) represents an emerging environmental challenge. While conventional plastics such as low-density polyethylene (LDPE) persist for decades, biodegradable alternatives like polybutylene adipate terephthalate (PBAT) are promoted as eco-friendly solutions. However, their environmental safety for crop plants and soil microbiota remains poorly understood. In this study, we evaluated the effects of LDPE and PBAT microplastics (1% w/w) on the growth and physiological state of winter wheat (Triticum aestivum L.) cultivated in soil, either alone or in combination with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) and the plant-beneficial fungus Trichoderma citrinoviride. Growth parameters (root and shoot length and mass), germination index, chlorophyll content, antioxidant enzyme activity, and lipidomic profiles of wheat were assessed. PBAT stimulated biomass accumulation but simultaneously triggered oxidative stress and remodeled membrane phospholipids, indicating physiological disturbance. T. citrinoviride enhanced wheat growth and mitigated oxidative stress under non-contaminated conditions; however, its beneficial effect was generally suppressed in the presence of PBAT and/or 2,4-D. The results suggest that, despite its biodegradability, PBAT may pose a higher phytotoxic potential than conventional LDPE, particularly by altering oxidative balance and membrane lipid composition in wheat. Full article

Sewage sludge is increasingly recognized as a major reservoir for pharmaceuticals and emerging contaminants that are only partially removed by conventional wastewater treatment. This study provides the first comprehensive assessment of these contaminants in biosolids generated from ten major wastewater treatment plants (WWTPs) across Jordan. Different pharmaceuticals were quantified in the sludge samples generated. The results revealed concentrations ranging from 10 to over 2000 µg kg⁻¹, with antibiotics typically showing the highest enrichment (e.g., ciprofloxacin up to 2165 µg kg⁻¹, ofloxacin up to 303 µg kg⁻¹). Anti-inflammatory compounds such as diclofenac reached 196 µg kg⁻¹, while the antimicrobial triclosan exceeded 4700 µg kg⁻¹ in some sludge samples. Carbamazepine, a recalcitrant antiepileptic drug, ranged between 50 and 223 µg kg⁻¹, reflecting both widespread use and strong persistence. Elevated levels of quaternary ammonium compounds (QACs) were also detected. The highest levels were generally associated with large urban WWTPs and plants receiving industrial discharges. Environmental risk assessment (ERA) indicated that the risk for soil biota was acceptable for most cases for low application doses (5–10 t/ha) except for WWTP6-MD, WWTP8-S, and WWTP9-IC, where the risk was non-acceptable. Severe limitations in the risk assessment were noted: reliable toxicity endpoints in terrestrial soil organisms such as microbiota, collembola, and earthworms are few, while deriving endpoints via aquatic available data is not always reliable. Overall, the findings demonstrate that Jordanian sewage sludge contains environmentally relevant levels of pharmaceuticals and QACs and that risk assessment is, therefore, pertinent before any stabilization and realistic land application scenarios are chosen. Full article

The Qaidam Basin on the Qinghai–Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity—the capacity to shift metabolic profiles independently of taxonomic turnover—in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation. Full article

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, and developmental plasticity. This review summarizes current evidence on how salinity remodels flavonoid biosynthesis, regulation, and function from cellular to whole-plant scales. We first outline the phenylpropanoid–flavonoid pathway, with emphasis on transcriptional control by MYB, bHLH, and NAC factors and their integration with ABA, JA, and auxin signaling. We then discussed how post-synthetic modifications such as glycosylation and methylation adjust flavonoid stability, compartmentation, and activity under salt stress. Functional sections highlight roles of flavonoids in ROS scavenging, Na⁺/K⁺ homeostasis, membrane integrity, and the modulation of ABA/MAPK/Ca²⁺ cascades and noncoding RNA networks. Spatial aspects, including root–shoot communication and rhizosphere microbiota recruitment, are also considered. Based on this synthesis, we propose a flavonoid-centered stress network (FCSN), in which specific flavonoids function as key nodes that connect metabolic flux with hormonal crosstalk and stress signaling pathways. We argue that reconceptualizing flavonoids as central stress network regulators, rather than generic antioxidants, provides a basis for metabolic engineering, bio-stimulant design, and breeding strategies aimed at improving crop performance on saline soils. Full article

Phosphate-solubilizing rhizobacteria associated with the Solanum tuberosum L. cultivar ‘Superchola’ were isolated and characterized to improve our understanding of plant growth promotion in agricultural systems. Bacteria were isolated by serial dilutions, and the morphology of the colonies was characterized on nutrient agar culture medium. In addition, morphological identification was achieved by Gram staining. The ability to solubilize phosphate was assessed in Pikovskaya agar culture medium, while molecular identification involved the amplification of the partial 16S rRNA gene using the polymerase chain reaction. In the Píllaro canton, the highest number of colony-forming units per gram of soil was recorded at 9.72 × 10⁹. Among the isolated strains, 62% exhibited circular morphology, 92% had a smooth texture, and 85% displayed entire margins. Notably, 83% of the isolates were Gram-negative, with 50% exhibiting a bacillary form. The most effective phosphate solubilizers were from the Mocha canton, particularly the isolate CC-FCAGP-BSF6, which showed superior solubilization capacity. Molecular identification revealed bacterial isolates from four genera, i.e., Bacillus, Pseudomonas, Lysinibacillus, and Paenibacillus. These strains exhibited significant phosphate solubilization in vitro and resulted in increased leaf area (0.21–0.49, p = 0.038), fresh mass (0.46–0.87, p = 0.014), dry mass (0.092–0.096, p = 0.047), and leaf area index (0.14–0.33, p = 0.026) in the S. tuberosum cultivar ‘Superchola’ in vitro plants. This study identifies bacterial species associated with the rhizosphere of S. tuberosum in Ecuador and highlights their potential for promoting plant growth and solubilizing phosphates. Full article

The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the “non-productive” and “productive” soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus–Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium–Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management. Full article

Reductive soil disinfestation (RSD) is an effective approach for controlling horticultural plant diseases by improving soil properties. However, its effects on microbial communities and their functional characteristics across soil depths remain poorly researched. In this study, we evaluated the impacts of RSD using solid (rice bran, RB) and liquid (molasses, MO) organic amendments in a Fusarium-infested field. Changes in biotic and abiotic properties were examined at two soil depths (0–15 cm and 15–30 cm) and the potential of different amendments to restore microecological functions in deeper soil was assessed. Both RSD treatments alleviated soil acidification and salinization compared with the control. The absolute abundances of Fusarium oxysporum and Fusarium solani were significantly reduced under both treatments, with MO-RSD showing stronger pathogen suppression in the 15–30 cm layer. MO-RSD exerted a greater influence on microbial community structure across soil depths, resulting in bacterial-fungal co-occurrence networks with higher complexity. Metabolic activity and carbon source utilization increased significantly following both RSD treatments, with the greatest enhancement observed in the 0–15 cm layer under MO-RSD. Furthermore, MO-RSD enriched a higher diversity and abundance of beneficial microorganisms such as Bacillus, Paenibacillus, and Tumebacillus in the 0–15 cm layer, and Azotobacter, Penicillium, and Neurospora in the 15–30 cm layer. These microbes were closely associated with enhanced metabolic activity and pathogen suppression. Overall, MO-RSD established a more integrated and functionally diverse microbiota across the 0–30 soil profile, likely due to the greater permeability and mobility of liquid organic amendments in shaping deeper soil microbial communities. Full article

The extensive and often inappropriate use of antibiotics has led to the rapid emergence and spread of antibiotic resistance, reducing their effectiveness against pathogenic microorganisms. Fosfomycin has become an increasingly important therapeutic option in both human and veterinary medicine, particularly when other antibiotics fail. This review summarises current knowledge on the occurrence of fosfomycin resistance and evaluates the role of agricultural practices in its dissemination. Multiple microbial resistance mechanisms have been identified, including genes from the fosA, fosB, and fosC families, and new determinants continue to be reported. Agriculture contributes to the environmental spread of resistance through the use of antibiotics in food-producing animals, the exchange of resistant microorganisms between humans and animals, and the application of manure as fertiliser. Fosfomycin resistance genes have been detected in livestock such as pigs, chickens, pigeons, and cows, as well as in vegetables. Their presence in soil is influenced by fertilisation, nitrogen levels, microplastics, heavy metals, and pesticide application. Additionally, climate warming may facilitate the broader dissemination of fosfomycin resistance. Despite increasing evidence, current understanding remains limited. Further research is needed to elucidate the mechanisms driving the spread of fosfomycin resistance in agricultural environments and to develop effective monitoring strategies. Full article

Long-term exposure of plastics to the environment causes them to disintegrate, resulting in the formation of micro/nanoplastics as well as the release of additives and chemicals into the soil. The micro/nanoplastics are able to readily migrate into the soil, destabilize the soil microbiota, and finally enter crop plants. Endocytosis, apoplastic transport, root adsorption, transpiration pull, stomatal entry, and crack-entry mode are well-known pathways by which microplastics enter into plants. Roots of vegetable crops were able to transfer 0.2 µm–1.0 µm of microplastics through root adsorption and by transpiration pull to the xylem and then further transported them to the plant tissues through apoplastic pathways. Beads of 1000 nm size were also engulfed by BY-2 protoplast cells through endocytosis. Micro and nanoplastics that enter crops affected the physiological and biochemical activities of the plants. Aquaporins were needed to aid the symplastic pathway which made the symplastic pathway difficult for MPs/NPs transport. Microplastics block seed capsules and roots of seedlings, thereby negatively affecting the uptake and efficient use of nutrients supplied. Photosynthesis of plants was affected due to the reduction in chlorophyll contents. Exposing soils to MPs/NPs drastically affected the pH, EC, and bulk density of the soil. This review focused on bridging the knowledge gap with understanding how microplastics prevent nutrient uptake and nutrient use efficiency in plants. This understanding is essential for assessing the broader ecological impacts of plastic contamination and for developing effective mitigation strategies. Further research is needed on microorganisms capable of degrading plastics, as well as on developing analytical methods for detecting plastics in soil and plant tissues. Also, further research on how to replace plastic mulching and still provide the same benefits as plastic mulch is needed. Full article

Suillus luteus is a highly prized edible fungus and demonstrates significant potential in the field of bioremediation, particularly for soil restoration and pollution mitigation. However, systematic research on the structural characteristics of the bioactive polysaccharides and regulatory effects on gut microbiota metabolism remains scarce. In this study, S. luteus polysaccharide (SLP) was obtained by hot water extraction and the structural characteristics were systematically determined, as well as the regulatory function on gut microbiota metabolism in a tumor-bearing mice model. Results showed that SLP exhibited an average molecular weight of approximately 1.90 × 10⁶ Da with Fuc:Man:Glc:Gal molar ratio of 0.37:1.00:0.72:0.54. The polysaccharide predominantly employed β-(1→4)-Manp as the backbone with α-(1→3)-Fucp, α-(1→6)-Glcp, and α-(1→6)-Galp as side chains. SLP administration of 200 mg/kg in tumor-bearing mice exerted enrichment effects of intestinal probiotics, including Lactobacillus and Odoribacter, which were associated with alterations in glyoxylate and dicarboxylic acid metabolism, ultimately enhancing CD4⁺ T cell immunity and resulting in a tumor suppression rate of 53.14%. This study provides a theoretical foundation and supporting data for the development of S. luteus polysaccharide in the functional food field. Full article

Invasive species are a recurring global problem, and the water hyacinth (Pontederia crassipes) is a well-known example. Various strategies have been explored to manage its spread, including its use as an agricultural amendment. However, when P. crassipes biomass is incorporated into soil and undergoes degradation, it may increase soil conductivity and promote metal leaching, potentially affecting soil biota, particularly microbiota. Saprophytic fungi play a key role in the decomposition and renewal of organic matter, and their resilience to stressors is crucial for maintaining soil function. Thus, the aim of this study was to evaluate the effects of P. crassipes biomass extracts on the saprophytic fungus Trametes versicolor by evaluating fungal growth and metabolic changes [including sugar content, phosphatase enzymatic activity, and reactive oxygen species (ROS) production]. The fungus was exposed for 8 days to a dilution series of extracts (100%—undiluted, to 3.13%) prepared from P. crassipes biomass collected at five locations in Portuguese wetlands. Two sites were in the south, within a Mediterranean climate (Sorraia and Estação Experimental António Teixeira), and three were in the north, within an Atlantic climate (São João de Loure, Pateira de Fermentelos, and Vila Valente), representing both agricultural-runoff–impacted areas and recreational zones. Extracts were used to simulate a worst-case scenario. All extracts have shown high conductivity (≥15.4 mS/cm), and several elements have shown a high soluble fraction (e.g., K, P, As, or Ba), indicating substantial leaching from the biomass to the extracts. Despite this, T. versicolor growth rates were generally not inhibited, except for exposure to the São João de Loure extract, where an EC₅₀ of 45.3% (extract dilution) was determined and a significant sugar content decrease was observed at extract concentrations ≥25%. Possibly due to the high phosphorous leachability, both acid and alkaline phosphatase activities increased significantly at the highest percentages tested (50% and 100%). Furthermore, ROS levels increased with increasing extract concentrations, yet marginal changes were observed in growth rates, suggesting that T. versicolor may efficiently regulate its intracellular redox balance under stress conditions. Overall, these findings indicate that the degradation of P. crassipes biomass in soils, while altering chemical properties and releasing soluble elements, may not impair and could even boost microbiota, namely saprophytic fungi. This resilience highlights the potential ecological benefit of saprophytic fungi in accelerating the decomposition of invasive plant residues and contribution to soil nutrient cycling and ecosystem recovery. Full article

Soil degradation and climate-driven stress increasingly compromise crop performance by disrupting microbial communities and weakening soil biological functions. Microbial consortia such as Effective Microorganisms (EM) are widely adopted as nature-based solutions to enhance soil health and plant productivity, yet it remains unclear whether their biostimulant effects arise primarily from microbial activity or from the metabolites they release. This study aimed to disentangle these contributions by comparing the effects of EM and its cell-free extract (EM Extract) on zucchini (Cucurbita pepo L.), grown under controlled conditions. Growth parameters and pigment composition were quantified through morphological and spectrophotometric analyses, while soil microbial communities and metabolic profiles were characterized using metabarcoding and high-resolution FTIR-based soil metabolomics. Both EM and EM-derived cell-free extracts significantly enhanced zucchini growth, increasing plant height, biomass, chlorophyll content and root development. Cultural-based microbial analyses showed complementary shifts in rhizosphere communities, yet no major taxonomic differences were detected. Consistently, both treatments induced similar metabolomic changes in bulk and rhizosphere soils, resulting in a shared functional state shaped by plant inputs. These results suggest EM extract as a stable and effective alternative to live microbial inoculants for sustainable crop bio stimulation. Full article

Peganum harmala (L.) Schrad., a perennial medicinal plant thriving in arid Moroccan soils, represents a natural reservoir of unexplored bacterial diversity. To uncover its hidden foliar endosphere microbiota, we isolated and characterized two Acinetobacter strains: a novel endophytic bacterium, AGC35, and another strain, AGC59, newly reported from this host. Both are non-halophilic, aerobic, Gram-negative bacteria exhibiting optimal growth at 30–35 °C, pH5, and with 1% NaCl. An integrative genomic, phylogenetic, functional, and phenotypic characterization classified both strains within the genus Acinetobacter (class Gamma-pseudomonadota). However, Average Nucleotide Identity (<96%) and digital DNA-DNA Hybridization (<70%) values distinguished the AGC35 strain as a novel species, for which the name Acinetobacter endophylla sp. nov. is proposed. A comparative genomic and phenotypic analysis with the co-isolated Acinetobacter pittii strain AGC59 revealed extensive genome rearrangements, reflecting distinct evolutionary lineage and ecological strategies. While both genomes share core metabolic pathways, A. endophylla harbors specialized genes for the degradation of plant-derived aromatic compounds (e.g., catechol) but shows reduced capacities in carbohydrate metabolism and osmotic stress tolerance, traits indicative of a metabolic specialist with plant-growth-promotion potential, including phosphorus, potassium, and silicon solubilization and indole-3-acetic acid production. In contrast, A. pittii exhibits a more generalist genome enriched in stress functions. Analysis using the Antibiotics and Secondary Metabolite Analysis Shell revealed multiple biosynthetic gene clusters in both strains, showing ≤26% similarity to known references, suggesting the potential for novel antimicrobial secondary metabolite biosynthesis, including antifungal lipopeptides and thiopeptide antibiotics. Altogether, functional specialization and ecological coherence of these findings support the recognition of A. endophylla sp. nov. as a genomically and functionally distinct species, highlighting niche partitioning and adaptive metabolism within the P. harmala holobiont. These results underscore the plant’s value as a reservoir of untapped microbial diversity with significant ecological and biotechnological relevance. Finally, future work will focus on elucidating the novel metabolites encoded by the biosynthetic gene clusters in both isolates and exploring their applications in crop-improvement strategies and natural-product discovery. Full article

Analysis of the apple tree rhizosphere and phylloplane microbiota revealed the presence of pathogenic and conditionally pathogenic micromycetes: Penicillium, Cladosporium, Fusarium, Mucor, Trichotecium, Alternaria. The application of microbial fertilizers (MFs)—Azafok, Enzymocid, and Nitragin—reduced their abundance in the soil. This occurred due to the beneficial bacteria contained in the biopreparations (Bacillus spp., Bacillus aryabhattai, Pseudomonas fluorescens, Bradyrhizobium japonicum), which possess fungicidal activity and the ability to improve the mineral nutrition of plants, thereby enhancing their immune status. Nitragin also reduced the colonization of leaves by pathogenic fungi. The greatest reduction in contamination was achieved by the combined application of MFs with foliar feeding using mineral substances, particularly when using Azafok. The influence of MFs on the state of the epiphytic microbiota is associated with their indirect action through the activation of the host plant’s functional activity and the stimulation of its defense mechanisms. The MFs introduced into the soil stimulated an increase in the content of nitrogen, phosphorus, potassium, and calcium in the leaves. We also noted the influence of MFs on modifying the effect of foliar feeding on the nutrient content in the leaves. The leaf nitrogen content with the combined application of soil-applied Azafok and FF was lower than with soil application alone. Furthermore, the use of foliar fertilizing reduced the phosphorus and potassium content in the leaves against the background of Azafok and Enzymocid, although the relative level of these nutrient contents remained very high. Only the application of foliar fertilizing against the background of Nitragin stimulated an increase in the phosphorus and potassium content in the leaves. Further research is needed to clarify the nature of this modification. Full article