Search Results (231)

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

Glycyrrhiza uralensis (G. uralensis), a leguminous plant, is an important medicinal and economic plant in saline–alkaline soils of arid regions in China. Its main bioactive components include liquiritin, glycyrrhizic acid, and flavonoids, which play significant roles in maintaining human health and preventing and adjuvantly treating related diseases. However, the cultivation of G. uralensis is easily restricted by adverse soil conditions in these regions, characterized by high salinity, high alkalinity, and nutrient deficiency. This study investigated the impacts of four multistrain microbial inoculants (Pa, Pb, Pc, Pd) on the growth performance and bioactive compound accumulation of G. uralensis in moderately saline–sodic soil. The aim was to screen the most beneficial inoculant from these strains, which were isolated from the rhizosphere of plants in moderately saline–alkaline soils of the Hexi Corridor and possess native advantages with excellent adaptability to arid environments. The results showed that inoculant Pc, comprising Pseudomonas silesiensis, Arthrobacter sp. GCG3, and Rhizobium sp. DG1, exhibited superior performance: it induced a 0.86-unit reduction in lateral root number relative to the control, while promoting significant increases in single-plant dry weight (101.70%), single-plant liquiritin (177.93%), single-plant glycyrrhizic acid (106.10%), and single-plant total flavonoids (107.64%). Application of the composite microbial inoculant Pc induced no significant changes in the pH and soluble salt content of G. uralensis rhizospheric soils. However, it promoted root utilization of soil organic matter and nitrate, while significantly increasing the contents of available potassium and available phosphorus in the rhizosphere. High-throughput sequencing revealed that Pc reorganized the rhizospheric microbial communities of G. uralensis, inducing pronounced shifts in the relative abundances of rhizospheric bacteria and fungi, leading to significant enrichment of target bacterial genera (Arthrobacter, Pseudomonas, Rhizobium), concomitant suppression of pathogenic fungi, and proliferation of beneficial fungi (Mortierella, Cladosporium). Correlation analyses showed that these microbial shifts were linked to improved plant nutrition and secondary metabolite biosynthesis. This study highlights Pc as a sustainable strategy to enhance G. uralensis yield and medicinal quality in saline–alkali ecosystems by mediating microbe–plant–nutrient interactions. Full article

Nanomaterials have emerged as a transformative technology in agricultural science, offering innovative solutions to improve plant–microbe interactions and crop productivity. The unique properties, such as high surface area, tunability, and reactivity, of nanomaterials, including nanoparticles, carbon-based materials, and electrospun fibers, render them ideal for applications such as nutrient delivery systems, microbial inoculants, and environmental monitoring. This review explores various types of nanomaterials employed in agriculture, focusing on their role in enhancing microbial colonization and soil health and optimizing plant growth. Key nanofabrication techniques, including top-down and bottom-up manufacturing, electrospinning, and nanoparticle synthesis, are discussed in relation to controlled release systems and microbial inoculants. Additionally, the influence of surface properties such as charge, porosity, and hydrophobicity on microbial adhesion and colonization is examined. Moreover, the potential of nanocoatings and electrospun fibers to enhance seed protection and promote beneficial microbial interactions is investigated. Furthermore, the integration of nanosensors for detecting pH, reactive oxygen species, and metabolites offers real-time insights into the biochemical dynamics of plant–microbe systems, applicable to precision farming. Finally, the environmental and safety considerations regarding the use of nanomaterials, including biodegradability, nanotoxicity, and regulatory concerns, are addressed. This review emphasizes the potential of nanomaterials to revolutionize sustainable agricultural practices by improving crop health, nutrient efficiency, and environmental resilience. Full article

Viticulture is vital to Italy’s agricultural sector, since it significantly contributes to the global wine industry. Microflora and microfauna are considered important factors for soil quality, improving grapevine growth, and promoting resistance to biotic and abiotic stresses. This study examined the impact of selected Trichoderma strains (T. harzianum M10 and T. afroharzianum T22) and their secondary metabolite 6-pentyl-α-pyrone (6PP) on the soil microbiome, the metabolome, and physiological changes of grapevines. Before treatment application, low levels of plant-parasitic nematodes (Rotylenchulus spp., Xiphinema pachtaicum) were found in the soil, together with pathogens (Fusarium spp., Neonectria spp.) and beneficial microbes (Clonostachys rosea, Pseudomonas spp.). Metagenomic analysis revealed significant treatment impacts in the soil microbiome, with T22 and 6PP treatments increasing Proteobacteria abundance, while slight variations of fungal communities and no significant differences in nematofauna were found. Metabolomic analysis showed that treatments induced grapevines to produce antioxidant secondary metabolites able to boost plant defense against abiotic and biotic stresses and increase nutraceutical grapes’ value. Finally, T22 treatment increased the grapes’ winemaking value, raising their Brix grade. Our results demonstrate that microbial or metabolite-based treatments could affect the soil microbiome composition, grapevine health and resilience, and grapes’ oenological and nutraceutical properties. Full article

Integrating organic soil amendments such as vermicompost (VC) and vermicompost tea (VCT) in agriculture has received increasing attention as a sustainable strategy to improve soil fertility, enhance plant growth, and suppress pest infestations. This study aimed to evaluate the effects of varying concentrations of VCT (10%, 20%, and 40%), alone and in combination with VC (2.47 ton/ha), on the development and yield of corn (Zea mays), and suppression of fall armyworm (FAW, Spodoptera frugiperda) infestation. The experiment was conducted in seven raised beds with seven treatments: V0 (control), VCT10, VCT20, VCT40, VC1 + VCT10, VC1 + VCT20, and VC1 + VCT40. Six weekly applications of VCT were applied starting at the V2 stage, and soil and plant nutrient contents were determined post-harvest. Additionally, relative chlorophyll content, height, cob yield, dry biomass, and FAW infestations were assessed. Results show that both VC and VCT significantly enhanced soil nutrient content compared to the control treatment (V0). VCT20 and VC1 + VCT10 improved plant N, K, and micronutrient uptake. Corn treated with VCT10 and VC1 + VCT10 had the highest biomass (6.52 and 6.57 tons/ha, respectively), while VCT20 produced the highest cob yield (6.0 tons/ha), which was more than eight times that of V0. SPAD values and corn height were significantly high across all treatments, with VCT20 achieving the highest SPAD readings while the control achieved the lowest. For FAW infestation, the control treatment experienced moderate infestation. At the same time, there was complete suppression in VCT20 and VCT40 treatments and a reduction in VC + VCT treatments, likely due to the bioactive compounds and beneficial microbes in VC and VCT that strengthened plant immunity. The results suggest that VCT20 is a cost-effective, eco-friendly amendment for improving corn performance and FAW resistance. This study contributes to sustainable agriculture by demonstrating how organic amendments can enhance crop resilience while supporting environmentally friendly farming practices. Full article

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

Urban soils are subject to intense anthropogenic disturbance, often resulting in biodiversity loss and reduced ecosystem functionality. However, rhizospheric microbial communities help maintain critical soil-ecosystem services, supporting urban soil resilience. This study evaluated the diversity of culturable bacteria associated with the rhizospheres of Pennisetum clandestinum and Pseudelephantopus spicatus in green areas of Medellín, Colombia, under contrasting levels of anthropic pressures. Rhizospheric and non-rhizospheric soils were sampled near automotive mechanic sites, and bacterial communities were assessed through plate counting and morphological characterization. Alpha, beta, and rarefaction diversity indices were applied to evaluate culturable morphotypes. P. clandestinum supported a more diverse and complex rhizospheric microbiome, particularly in non-exposed soils, while P. spicatus hosted less diverse communities under similar conditions. Diversity indices effectively distinguished microbial patterns, demonstrating the utility of culture-based methods for microbial community assessment. As a first step in microbial bioprospecting workflows, these methods allow for the rapid screening of culturable diversity and support decision-making for the selection of promising environments, plant species, and microbial isolates. This approach can inform urban soil threats, the promotion of beneficial plant–microbe interactions, and the identification of bioindicator species for soil health monitoring in a framework for the management of green areas. Full article

Disease-suppressive soils confer fitness advantages to plants after a disease outbreak due to the subsequent assembly of protective microbiota in natural environments. However, the role of ecological effects on the assemblage of a protective soil microbiome is largely elusive. In this study, we investigated the composition of parasitic microbes and their relationships with soybean cyst nematodes in suppressive soil. The results showed that parasitic microbial assembly along soybean cyst nematodes was shaped predominantly by the density of soybean cyst nematodes. We also found soybean continuous cropping increased the number of parasitic microbes of soybean cyst nematodes with the order of Ss > Sr > Sc, while it decreased the population of soybean cyst nematodes, resulting in a natural decline in the number of soybean cyst nematodes. These findings indicate that the population of soybean cyst nematodes accumulated parasitic microorganisms against this soil-borne disease under soybean long-term continuous cropping. Moreover, the metabolic activity of cyst parasitic microbes was increased by two years of continuous cropping (Sc) of soybean, and total carbon and total nitrogen of soil were the main impact factors in this short-term continuous cropping for metabolic patterns of the cyst parasitic microbes. In summary, the results highlight that the interaction of plants and disease shape the soil microbiome, recruit a group of disease resistance-inducing microbes, and modulate their beneficial traits to protect the plant. Full article

Cerium dioxide nanoparticles (CeO₂-NPs) are increasingly used in various industrial applications, leading to their inevitable release into the environment including the soil ecosystem. In soil, CeO₂-NPs are taken up by plants, translocated, and accumulated in plant tissues. Within plant tissues, CeO₂-NPs have been shown to interfere with critical metabolic pathways, which may affect plant health and productivity. Moreover, their presence in soil can influence soil physico-chemical and biological properties, including microbial communities within the rhizosphere, where they can alter microbial physiology, diversity, and enzymatic activities. These interactions raise concerns about the potential disruption of plant–microbe symbiosis essential for plant nutrition and soil health. Despite these challenges, CeO₂-NPs hold potential as tools for enhancing crop productivity and resilience to stress, such as drought or heavy metal contamination. However, understanding the balance between their beneficial and harmful effects is crucial for their safe application in agriculture. To date, the overall impact of CeO₂-NPs on soil -plant system and the underlying mechanism remains unclear. Therefore, this review analyses the recent research findings to provide a comprehensive understanding of the fate of CeO₂-NPs in soil–plant systems and the implications for soil health, plant growth, and agricultural productivity. As the current research is limited by inconsistent findings, often due to variations in experimental conditions, it is essential to study CeO₂-NPs under more ecologically relevant settings. This review further emphasizes the need for future research to assess the long-term environmental impacts of CeO₂-NPs in soil–plant systems and to develop guidelines for their responsible use in sustainable agriculture. Full article

American ginseng (AG) cultivation suffers from severe diseases, requiring heavy pesticide use. This study aimed to explore whether companion planting with maize (AG-maize) or Perilla frutescens (AG-perilla) could enhance AG growth and alter rhizosphere/root microbiomes in a root rot-infested field. Compared to monoculture (CK), companion planting significantly improved AG growth and survival rate at wither stage, with AG-maize showing the superior efficacy- increasing root length and fresh weight, and plant height by 39.04%, 46.10%, and 48.69%, respectively, while raising survival rate from 1.51% to 14.54%. Microbial analysis revealed that companion planting increased microbiome diversity and network complexity. At green fruit stage, AG-perilla increased rhizosphere fungal Chao1 index by 42.6%, while AG-maize and AG-perilla elevated endophytic fungal Shannon indices by 46.68% and 74.84%, respectively. At wither stage, AG-maize notably enriched beneficial microbes (e.g., soil Pseudomonas +108.49%, Bacillus +200.73%) while reducing pathogens (soil Fusarium −20.04%, root endophytic Alternaria −54.55%). Structural equation model indicated AG-maize improved AG survival via core species-driven antibiosis and nutrient regulation, with keystone species Lysobacter sp. RHLT3-4 and Verrucomicrobium sp. IMCC25902 significantly correlating with AG health. The AG-maize system fostered synergistic microbial networks, enriching beneficial taxa and suppressing pathogens. These findings provide a foundation for developing eco-friendly disease management and high-yield AG cultivation strategies. Full article

The morphogenesis and defense evolution of plants are intricately linked to soil microbial community dynamics, where beneficial and pathogenic bacteria regulate ecosystem stability through chemical signaling. A microbial communication mechanism known as quorum sensing (QS), which affects population density, virulence, and biofilm formation, substantially impacts plant development and immune responses. However, plants have developed strategies to detect and manipulate QS signals, enabling bidirectional interactions that influence both plant physiology and the balance of the microbiome. In this review, QS signals from bacteria, fungi, and nematodes are systematically examined, emphasizing their recognition by plant receptors, downstream signaling pathways, and the activation of defense responses. Most significantly, attention is given to the role of fungal and nematode QS molecules in modulating plant microbe interactions. By elucidating these communication networks, we highlight their potential applications in sustainable agriculture, offering novel insights into crop health management and ecosystem resilience. Full article

In Gannan navel orange (Citrus sinensis) orchards—a typical sloped farmland ecosystem—selected native grasses outperform conventional green manure due to their stronger ecological adaptability and lower management requirements. However, few studies have investigated how native grasses enhance soil organic carbon and nitrogen contents at the soil aggregate level. A 5-year field study was carried out to analyze the impacts of the native grasses practice on the accumulation of soil organic carbon and nitrogen and the physicochemical properties and microbial communities of soil aggregates in navel orange orchards. Three treatments were tested: (i) clean tillage (CK); (ii) intercropping Centella asiatica (L.) Urban (CA); (iii) intercropping Stellaria media (L.) Cvr. (SM). Our work found that, compared to CK, the soil physical properties improved under the long-term management of native grasses, and the content of nutrients in the soil increased. The contents of SOC (+118.3–184.2%) and total nitrogen (TN) (+73.3–81.5%) changed significantly. The proportion of soil macro-aggregates and the stability of soil aggregates increased, and the contents of SOC and TN in the soil aggregates increased. In addition, under the long-term management of native grasses, the community diversity of beneficial microbes and the abundance of functional genes related to nitrogen cycling increased significantly in the soil aggregates. Native grasses increased the content of nutrients in the soil aggregates by increasing aggregate stability and the abundance of related microorganisms, altering the microbial community structure, and increasing the abundance of related genes for nutrient cycling, thereby enhancing the sequestration of SOC and TN in topsoil. Our results will provide a theoretical basis for the carbon enhancement and fertilization of native grasses as green manure in navel orange orchards and their popularization and application. Full article

Biofertilizers play a crucial role in promoting sustainable agriculture in China; however, comprehensive quantification of their effects and limitations in field conditions remain unclear. In this study, a meta-analysis encompassing 1818 comparisons from 107 studies was conducted to quantify their systematic effects in field conditions in China. The results demonstrated that biofertilizers enhanced crop yields across 21 of the 23 investigated crops, with notable increases in millet (+65.42%), vegetables (e.g., Chinese cabbage +35.57%, ginger +39.18%), and legumes (kidney beans +54.03%), while cotton and rapeseed showed non-significant improvements. Nutritional quality was also improved, as evidenced by elevated levels of vitamin C (14.61%), protein (16.61%), and carotenoids (15.18%), alongside a reduction in nitrate content (21.94%). Soil health was significantly improved through increased organic matter (16.64%), enhanced enzymatic activities (urease: 57.60%; phosphatase: 43.51%), and a proliferation of beneficial microbes (bacteria: 157.10%; fungi: 30.28%), while pathogenic organisms were suppressed by 51.81%. The observed yield improvements were attributed to enhanced nutrient availability (total nitrogen: 16.67%; available phosphorus: 10.98%), optimized root growth (19.23% increase in volume), and a reduction in disease incidence (42.52%). The efficacy of biofertilizers was maximized when they were used in conjunction with organic amendments, resulting in a 29.20% increase in yield, particularly when applied prior to planting. These results show that biofertilizers boost productivity, quality, and soil functionality, depending on their production and field management practices. Their effectiveness is tied to optimizing soil properties and suppressing pathogens, providing strategies for sustainable agriculture in China. Full article

The increasing global population and intensifying resource limitations present a formidable challenge for sustainable crop production, especially in developing regions. This review explores the pivotal role of microbial ecosystem services in alleviating environmental stresses that impede agricultural productivity. Soil microbiota, particularly plant growth-promoting microbes (PGPMs), are integral to soil health and fertility and plant resilience against both abiotic (drought, salinity, temperature extremes, heavy metals) and biotic (pathogen) stresses. These microorganisms employ a variety of direct and indirect mechanisms, including the modulation of phytohormones, nutrient solubilization, the production of stress-alleviating enzymes, and the synthesis of antimicrobial compounds, to enhance plant growth and mitigate adverse environmental impacts. Advances in microbial biotechnology have expanded the toolkit for harnessing beneficial microbes, enabling the development of microbial inoculants and consortia tailored for specific stress conditions. This review highlights the multifaceted contributions of soil microbes, such as improving nutrient uptake, promoting root development, facilitating pollutant degradation, and supporting carbon sequestration, all of which underpin ecosystem resilience and sustainable agricultural practices. Furthermore, the synergistic interactions between plant roots and rhizospheric microbes are emphasized as key drivers of soil structure enhancement and long-term productivity. By synthesizing current research on the mechanisms of microbe-mediated stress tolerance, this review underscores the potential of microbial interventions to bridge the gap between food security and environmental conservation. The integration of microbial solutions into agroecosystems offers a promising, eco-friendly strategy to revitalize soils, boost crop yields, and ensure agricultural sustainability in the face of mounting environmental challenges. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article