Search Results (405)

Background/Objectives: Actinobacteria are one of the largest bacterial phyla. These microbes produce bioactive compounds, such as antifungals, antibiotics, immunological modulators, and anti-tumor agents. Studies on actinobacteria isolated from the Brazilian Savannah biome (Cerrado) are scarce and mostly address metagenomics or the search for hydrolytic enzyme-producing microbes. Solanum lycocarpum (lobeira) is a tree widely employed in regional gastronomy and pharmacopeia in Central Brazil. Methods: In this work, 60 actinobacteria isolates were purified from the rhizosphere of S. lycocarpum. Eight Streptomyces spp. isolates were selected for in vitro antifungal activity against Cryptococcus neoformans H99, the C. neoformans 89-610 fluconazole-tolerant strain, C. gattii NIH198, Candida albicans, C. glabrata, and C. parapsilosis. The ability of the aqueous extracts of the isolates to induce the in vitro secretion of tumor necrosis factor (TNF-α), nitric oxide (NO), interleukin-6 (IL-6), and IL-10 by murine macrophages was also evaluated. Results: All extracts showed antifungal activity against at least two yeast species. Streptomyces spp. LAP11, LDB2, and LDB17 inhibited C. neoformans growth by 40–93%. Most extracts (except LAP2) also inhibited C. gattii. None inhibited C. albicans, but all inhibited C. glabrata (40–90%). Streptomyces sp. LAP8 extract increased nitric oxide production by approximately 347-fold in murine macrophages, while LDB11 extract suppressed LPS-induced TNF-α production by 70% and simultaneously increased IL-10 secretion, suggesting immunosuppressive potential. Conclusions: The results revealed that Cerrado actinobacteria-derived aqueous extracts are potential sources of antifungal and immunomodulatory biocompounds. Full article

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

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

Plant-essential phosphorus (P) is a sparingly available mineral in soils. Phosphorus fertilizers—produced by the transformation of insoluble to soluble phosphates—are thus applied to agroecosystems. With advancements in commercial agriculture, crops have been increasingly adapted to grow in fertile environments. Wild crop relatives, however, are adapted to grow in unfertilized soils. In response to these two conditions of P bioavailability (fertilized agroecosystems and unfertilized natural soils), domesticated crops and wild species employ different strategies to grow and develop. It is essential to understand strategies related to P acquisition that may have been lost to domestication, and here we present, for the first time, that across species, modern cultivars engage in physical (i.e., root morphological) mechanisms while their wild relatives promote ecological (i.e., root-microbial) mechanisms. Domesticated crops showcase shallower root system architecture and engage in topsoil foraging to acquire P from the nutrient-stratified environments common to fertilized agroecosystems. Wild species associate with P-cycling bacteria and AM fungi. This divergence in P recovery strategies is a novel delineation of current research that has implications for enhancing agricultural sustainability. By identifying the traits related to P recovery that have been lost to domestication, we can strengthen the P recovery responses by modern crops and reduce P fertilization. Full article

Azospirillum is a well-studied genus of plant growth-promoting rhizobacteria (PGPR) and one of the most extensively researched diazotrophs. This genus can colonize rhizosphere soil and enhance plant growth and productivity by supplying essential nutrients to the host. Azospirillum–plant interactions involve multiple mechanisms, including nitrogen fixation, the production of phytohormones (auxins, cytokinins, indole acetic acid (IAA), and gibberellins), plant growth regulators, siderophore production, phosphate solubilization, and the synthesis of various bioactive molecules, such as flavonoids, hydrogen cyanide (HCN), and catalase. Thus, Azospirillum is involved in plant growth and development. The genus Azospirillum also enhances membrane activity by modifying the composition of membrane phospholipids and fatty acids, thereby ensuring membrane fluidity under water deficiency. It promotes the development of adventitious root systems, increases mineral and water uptake, mitigates environmental stressors (both biotic and abiotic), and exhibits antipathogenic activity. Biological nitrogen fixation (BNF) is the primary mechanism of Azospirillum, which is governed by structural nif genes present in all diazotrophic species. Globally, Azospirillum spp. are widely used as inoculants for commercial crop production. It is considered a non-pathogenic bacterium that can be utilized as a biofertilizer for a variety of crops, particularly cereals and grasses such as rice and wheat, which are economically significant for agriculture. Furthermore, Azospirillum spp. influence gene expression pathways in plants, enhancing their resistance to biotic and abiotic stressors. Advances in genomics and transcriptomics have provided new insights into plant-microbe interactions. This review explored the molecular mechanisms underlying the role of Azospirillum spp. in plant growth. Additionally, BNF phytohormone synthesis, root architecture modification for nutrient uptake and stress tolerance, and immobilization for enhanced crop production are also important. A deeper understanding of the molecular basis of Azospirillum in biofertilizer and biostimulant development, as well as genetically engineered and immobilized strains for improved phosphate solubilization and nitrogen fixation, will contribute to sustainable agricultural practices and help to meet global food security demands. Full article

Plant growth-promoting rhizobacteria (PGPR) are beneficial rhizosphere microorganisms for plants. They can promote plant absorption of nutrients, inhibit pathogenic microorganisms, enhance plant tolerance to abiotic and biotic stresses, and improve plant growth. Isolating new beneficial microbes and elucidating their promoting mechanisms can facilitate the development of microbial fertilizers. This study combined transcriptome sequencing and related experiments to analyze the mechanism by which the endophytic fungus ‘BF-F’ promotes the growth of Sesuvium portulacastrum. We inoculated the ‘BF-F’ fungus beside S. portulacastrum seedlings as the experimental group. Meanwhile, S. portulacastrum seedlings not inoculated with ‘BF-F’ were set as the control group. After inoculation for 0 d, 7 d, 14 d, 21 d, and 28 d, the plant height and the number of roots were measured. Furthermore, transcriptome sequencing on the roots and leaves of the S. portulacastrum was conducted. Differentially expressed genes were screened, and KEGG enrichment analysis was performed. Nitrogen metabolism-related genes were selected, and qRT-PCR was conducted on these genes. Furthermore, we analyzed the metabolomics of ‘BF-F’ and its hormone products. The results showed that inoculation of ‘BF-F’ significantly promoted the growth of S. portulacastrum. After ‘BF-F’ inoculation, a large number of genes in S. portulacastrum were differentially expressed. The KEGG pathway enrichment results indicated that the ‘BF-F’ treatment affected multiple metabolic pathways in S. portulacastrum, including hormone signal transduction and nitrogen metabolism. The auxin signaling pathway was enhanced because of a decrease in AUX expression and an increase in ARF expression. Contrary to the auxin signal transduction pathway, the zeatin (ZT) signaling pathway was suppressed after the ‘BF-F’ treatment. ‘BF-F’ increased the expression of genes related to nitrogen metabolism (NRT, AMT, NR, and GAGOT), thereby promoting the nitrogen content in S. portulacastrum. The metabolites of ‘BF-F’ were analyzed, and we found that ‘BF-F’ can synthesize IAA and ZT, which are important for plant growth. Overall, ‘BF-F’ can produce IAA and enhance the nitrogen use efficiency of plants, which could have the potential to be used for developing a microbial fertilizer. Full article

Peach fruit flesh spongy tissue disorder causes dry, porous, and brown areas in the flesh, severely compromising fruit quality and market value. While soil properties and calcium nutrition have been linked to the disorder, the role of rhizosphere microbial communities in disorder resistance remains unclear. This study investigated both the physicochemical properties and the root-associated microbiomes of disordered (CK) and healthy (TT) peach orchards to explore microbial mechanisms underlying disorder suppression. TT soils exhibited higher pH, greater organic matter, increased exchangeable calcium, and more balanced trace elements compared to CK. Microbial analysis revealed significantly higher diversity and enrichment of beneficial taxa in TT associated with plant growth and disorder resistance. Functional gene prediction showed TT was enriched in siderophore production, auxin biosynthesis, phosphate solubilization, and acetoin–butanediol synthesis pathways. Co-occurrence network analysis demonstrated that TT harbored a more complex and cooperative microbial community structure, with 274 nodes and 6013 links. Metagenomic binning recovered high-quality MAGs encoding diverse resistance and growth-promoting traits, emphasizing the ecological roles of Gemmatimonadaceae, Reyranella, Nitrospira, Bacillus megaterium, and Bryobacteraceae. These findings highlight the combined importance of soil chemistry and microbiome structure in disorder suppression and provide a foundation for microbiome-informed soil management to enhance fruit quality and promote sustainable orchard practices. Full article

Phosphate-solubilizing microbes (PSMs) in soil play a crucial role in converting insoluble phosphates into plant-available soluble phosphorus. This paper systematically presents a comprehensive array of qualitative and quantitative techniques to assess the phosphate-decomposing capabilities of microbes. Additionally, it introduces two optimized media, namely improved Monkina medium No. 1 and No. 2, which are particularly suitable for detecting the solubilization abilities of microbes toward insoluble organic phosphates. Talaromyces nanjingensis, a novel fungal species recently isolated from the rhizosphere soil of Pinus massoniana, demonstrates remarkable phosphate-solubilizing abilities. Across multiple temperature gradients (15 °C, 20 °C, 25 °C, 30 °C, and 37 °C), it effectively decomposes both insoluble inorganic and organic phosphates. This is achieved through the secretion of organic acids, including gluconic acid (6.10 g L⁻¹), oxalic acid (0.93 g L⁻¹), and malonic acid (0.17 g L⁻¹), as well as phosphate-solubilizing enzymes. Moreover, under low-, medium-, and high-temperature conditions, T. nanjingensis can decompose insoluble phosphates in three types of soil with varying pH levels, thereby enhancing the overall soil fertility. Genomic analysis of T. nanjingensis has identified approximately 308 genes associated with phosphate decomposition and environmental adaptability, validating its superior capabilities and multi-faceted strategies for phosphate mobilization. These findings underscore the wide applicability of T. nanjingensis in maintaining soil phosphorus homeostasis and optimizing the phosphorus use efficiency, highlighting its promising potential for agricultural and environmental applications. Full article

Waterlogging is a critical abiotic stressor that significantly impacts plant growth. Plants under waterlogging stress release metabolic signals that recruit rhizosphere microorganisms and enhance stress resistance. However, the mechanisms through which the non-adaptive species R. delavayi responds to waterlogging stress via the synergistic interaction between root metabolites and rhizosphere microbiota remain poorly elucidated. Here, we employed pot experiments to characterize the responses of the root metabolite–microbiota complex in R. delavayi during waterlogging stress and subsequent recovery. Our results revealed that waterlogging altered the root morphology, the root metabolite profile, rhizosphere microbial diversity and network complexity, and these effects persisted during recovery. A significant correlation between root metabolites and the rhizosphere microbial community structure during waterlogging stress and recovery. Importantly, some differentially accumulated metabolites had significant effects on the assembly of rhizosphere microbes. Most of the core microbes in the rhizosphere microbial community under waterlogging and post–waterlogging recovery treatment were likely beneficial bacteria. Based on these findings, we propose a model for how root metabolites and rhizosphere microbes interact to help R. delavayi cope with waterlogging and recover. Based on these findings, we propose a possible response pattern of root metabolites and rhizosphere microbiota complex in R. delavayi under waterlogging stress and recovery. This work provides new insights into the synergistic mechanisms enhancing plant waterlogging tolerance and highlights the potential of harnessing rhizosphere microbiota to improve resilience in rhododendrons. 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

Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte–infected plants (E+) and Epichloë endophyte–free plants (E−) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E− groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO₃⁻-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E− plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E− plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E− plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth. Full article

Microbial interactions within the rhizosphere are fundamental to plant health, influencing nutrient availability, stress tolerance, and pathogen resistance. Beneficial microbes, such as plant growth-promoting microbes (PGPMs), including bacteria and mycorrhizal fungi, enhance plant resilience through mechanisms like nutrient solubilization, phytohormone production, and pathogen suppression via antimicrobial compounds and siderophores. Root exudates, composed of sugars, organic acids, and secondary metabolites, act as chemoattractants that shape the rhizosphere microbiome by recruiting beneficial microbes. Microbial metabolites can, in turn, modulate plant physiology and exudate profiles, thereby reinforcing mutualistic interactions. Stress conditions alter exudate composition, enabling plants to attract specific microbes that aid in stress mitigation. Given the growing interest in microbiome-based agricultural solutions, this review aims to synthesize recent literature on plant–microbe interactions, with a focus on bidirectional signaling between plants and microbes. A structured literature search was conducted using databases such as PubMed, Scopus, and ScienceDirect to identify key studies on root exudation, microbial functions, and synthetic microbial communities (SynComs). We highlight major findings on how engineered microbiomes can enhance plant growth, resilience, and productivity, particularly under stress conditions. This review also explores how advances in SynCom design can promote sustainable agriculture by reducing reliance on chemical inputs. 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