Search Results (81)

A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture. Full article

Soil salinization severely restricts crop growth and presents a major challenge to global agriculture. In this study, a plant-growth-promoting rhizobacterium (PGPR) was isolated and identified as Proteus sp. through 16S rDNA analysis and was subsequently named Proteus sp. JHY1. Under salt stress, exogenous dopamine (DA) significantly enhanced the production of indole-3-acetic acid and ammonia by strain JHY1. Pot experiments revealed that both DA and JHY1 treatments effectively alleviated the adverse effects of 225 mM NaCl on rice, promoting biomass, plant height, and root length. More importantly, the combined application of DA-JHY1 showed a significant synergistic effect in mitigating salt stress. The treatment increased the chlorophyll content, net photosynthetic rate, osmotic regulators (proline, soluble sugars, and protein), and reduced lipid peroxidation. The treatment also increased soil nutrients (ammoniacal nitrogen and available phosphorus), enhanced soil enzyme activities (sucrase and alkaline phosphatase), stabilized the ion balance (K⁺/Na⁺), and modulated the soil rhizosphere microbial community by increasing beneficial bacteria, such as Actinobacteria and Firmicutes. This study provides the first evidence that the synergistic effect of DA and PGPR contributes to enhanced salt tolerance in rice, offering a novel strategy for alleviating the adverse effects of salt stress on plant growth. Full article

The excessive use of chemical fertilizers in tea cultivation threatens soil health, environmental sustainability, and long-term crop productivity. This study explores the application of plant growth-promoting bacteria (PGPB) as an eco-friendly alternative to conventional fertilizers. A bacterial consortium was developed using selected rhizobacterial isolates—Lysinibacillus fusiformis, five strains of Serratia marcescens, and two Bacillus spp.—based on their phosphate and zinc solubilization abilities and production of ACC deaminase, indole-3-acetic acid, and siderophores. The consortium was tested in both pot and field conditions using two tea clones, S3A3 and TS491, and compared with a chemical fertilizer treatment. Plants treated with the consortium showed enhanced growth, biomass, and antioxidant activity. The total phenolic contents increased to 1643.6 mg GAE/mL (S3A3) and 1646.93 mg GAE/mL (TS491), with higher catalase (458.17–458.74 U/g/min), glutathione (34.67–42.67 µmol/gfw), and superoxide dismutase (679.85–552.28 units/gfw/s) activities. A soil metagenomic analysis revealed increased microbial diversity and the enrichment of phyla, including Acidobacteria, Proteobacteria, Actinobacteria, Chloroflexi, and Firmicutes. Functional gene analysis showed the increased abundance of genes for siderophore biosynthesis, glutathione and nitrogen metabolism, and indole alkaloid biosynthesis. This study recommends the potential of a PGPB consortium as a sustainable alternative to chemical fertilizers, enhancing both the tea plant performance and soil microbial health. Full article

Soil salinization poses a critical threat to global agriculture, necessitating innovative strategies for sustainable remediation. This review synthesizes advances in leveraging plant–microbe interactions to remediate saline–alkali soils, focusing on oilseed crops—Brassica napus, Glycine max, Arachis hypogaea, Helianthus annuus, and Sesamum indicum—as keystone species for ecosystem restoration. These crops exhibit unique adaptive strategies, including root architectural plasticity and exudate-mediated recruitment of stress-resilient microbiomes (Proteobacteria, Actinobacteria, and Ascomycota), which collectively stabilize soil structure and enhance nutrient cycling, ion homeostasis, and soil aggregation to mitigate soil salinity and alkalinity. Emerging technologies further amplify these natural synergies: nanomaterials optimize nutrient delivery and microbial colonization, while artificial intelligence (AI) models predict optimal plant growth-promoting rhizobacteria (PGPR) combinations and simulate remediation outcomes. This integration establishes a roadmap for precision microbiome engineering, offering scalable strategies to restore soil health and ensure food security in saline–alkali ecosystems. Full article

The gut microbiota, dominated by bacteria from the Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria phyla, plays an essential role in fermenting indigestible carbohydrates, regulating metabolism, synthesizing vitamins, and maintaining immune functions and intestinal barrier integrity. Dysbiosis is associated with obesity development. Shifts in the ratio of Firmicutes to Bacteroidetes, particularly an increase in Firmicutes, may promote enhanced energy storage, appetite dysregulation, and increased inflammatory processes linked to insulin resistance and other metabolic disorders. The purpose of this literature review is to summarize the current state of knowledge on the relationship between the development and treatment of obesity and overweight and the gut microbiota. Current evidence suggests that probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) can influence gut microbiota composition and metabolic parameters, including body weight and BMI. The most promising effects are observed with probiotic supplementation, particularly when combined with prebiotics, although efficacy depends on strain type, dose, and duration. Despite encouraging preclinical findings, FMT has shown limited and inconsistent results in human studies. Diet and physical activity are key modulators of the gut microbiota. Fiber, plant proteins, and omega-3 fatty acids support beneficial bacteria, while diets low in fiber and high in saturated fats promote dysbiosis. Aerobic exercise increases microbial diversity and supports growth of favorable bacterial strains. While microbiota changes do not always lead to immediate weight loss, modulating gut microbiota represents an important aspect of obesity prevention and treatment strategies. Further research is necessary to better understand the mechanisms and therapeutic potential of these interventions. Full article

This study aims to identify the optimal conditions—host, plant material, seasonality, and agricultural practices—for isolating and developing a collection of culturable endophytic microorganisms to support sustainable Olea europaea L. cultivation. Samples were collected from three Sicilian olive cultivars (‘Nocellara del Belice’, ‘Nocellara Etnea’, and ‘Nocellara Messinese’) and six wild olive accessions across different phenological phases and under organic and conventional agronomic management. Endophytes were isolated from leaves and twigs using a culture-dependent approach, and their taxonomic diversity and plant-growth-promoting (PGP) traits were analyzed. A total of 133 endophytic isolates were identified, spanning bacterial (Proteobacteria, Firmicutes, and Actinobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Wild olive trees contributed more than cultivated varieties to enriching the diversity and composition of culturable endophyte collection as well as twigs instead of leaves. Winter sampling allowed to implement the taxonomic genera of olive endophyte collection. Both farming systems favored an increase in the composition of microbial collection, though organic farming systems supported greater microbial richness. Functional analysis highlighted key PGP traits in a selection of bacterial isolates, including indole-3-acetic acid and siderophore production, nitrogen fixation, and antifungal activity. Bacillus spp. dominated enzymatic activities, such as amylase, protease, and lipase production, as well as antifungal activity against the olive fungal pathogen Neofusicoccum vitifusiforme. This research highlights the significant diversity and functional potential of Mediterranean olive endophytes. Our findings emphasize the role of native microbial communities as bio-inoculants, promoting plant growth, nutrient uptake, and disease resistance. These insights lay the groundwork for developing targeted olive-microbial consortia for biocontrol and stress tolerance applications. Full article

Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha⁻¹). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini–Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini–Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m³ ha⁻¹ of biogas and 284.4 L ha⁻¹ of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant–microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts. Full article

Straw return enhances soil biological properties by increasing carbon and energy availability, thereby improving conditions for microbial communities. However, the introduction of beneficial bacteria, such as Bacillus subtilis, can further shape the rhizosphere bacterial composition. In this study, we combined sugarcane straw return with B. subtilis inoculation to test whether this synergy reduces microbial specialization in the sugarcane rhizosphere. Three treatments were evaluated: (I) bulk soil (bulk), (II) rhizosphere soil with straw return but no B. subtilis inoculation (straw), and (III) rhizosphere soil with straw return and B. subtilis inoculation (straw + Bacillus). The bacterial community, including plant-growth-promoting bacteria (PGPB), was analyzed via 16S rRNA amplicon sequencing. Neither straw return nor B. subtilis inoculation significantly altered bacterial richness, diversity, or phylum-level abundance in the rhizosphere. Actinobacteria, Firmicutes, and Proteobacteria dominated the community, with Bacillus, Bradyrhizobium, and Paenibacillus as the predominant PGPB genera. Notably, only Bradyrhizobium abundance increased in the rhizosphere when straw was co-applied with B. subtilis. A co-occurrence network analysis revealed stronger microbial interactions under straw return, while B. subtilis enhanced connectivity among the PGPB. Although niche occupancy remained stable, PGPB specialization was higher with straw alone, suggesting that B. subtilis fosters a more generalist community. In conclusion, while straw return and B. subtilis inoculation did not affect overall bacterial diversity, B. subtilis increased PGPB interactions and reduced functional specialization, promoting a more generalized microbial community. Full article

This study aimed to examine the effect of adding volcanic slag to soil on the growth, yield, and quality of cucumbers. It also analyzed the changes in the physicochemical properties of the rhizosphere soil, as well as the diversity and structural changes of the bacterial community present in the soil of the cucumber plants. This study used conventional fertilization and cultivation techniques and set up five treatments: HS500, HS1000, HS1500, and HS2000 (representing 500, 1000, 1500, and 2000 kg/ha of volcanic slag added per 667 sq.m in the cultivation trough, respectively), and control (CK; representing 0 kg of added volcanic slag). The Illumina MiSeq System was used to analyze the soil microbial community. The findings revealed that the HS1000 treatment had the most significant promoting effect on increasing cucumber yield, whereas the HS2000 treatment exhibited no significant change compared with the CK treatment. The HS500, HS1000, and HS1500 treatments increased the yield by 12.89%, 24.28%, and 19.56%, respectively, compared with the CK treatment. The HS1000 treatment increased the soluble sugar, vitamin C, and soluble solid contents by 12.39%, 17.57%, and 24.33%, respectively, compared with the CK treatment. The organic matter, total nitrogen, alkali-hydrolyzable nitrogen, nitrate nitrogen, ammonium nitrogen (NH4+-N), available potassium (AK), and available phosphorus (AP) contents in the rhizosphere soil of cucumber plants were the highest under the HS1000 treatment. The alpha diversity analysis revealed that the Chao1, Shannon, and ACE indexes reached the highest under the HS1000 treatment, which were significantly higher than the CK treatment. In contrast, the Simpson index and coverage had no significant changes between treatments. The dominant phyla in each treatment were Proteobacteria, Actinobacteria, and Acidobacteria, among others. The redundancy analysis of soil physicochemical properties and 15 bacterial genera of interest revealed that the available phosphorus, available potassium, and NH4+-N contents were the primary factors influencing the bacterial community in cucumber rhizosphere soil. Full article

Undisturbed soils are essential ecosystems with high microbial diversity. Microorganisms present in the soil can regulate biogeochemical cycles, making available and transforming different minerals in the soil, such as nitrogen, phosphorus and sulfur. In this study, the microbiota of undisturbed soils was characterized using an integrated approach of 16S rRNA ribosomal gene amplicon analysis and classical microbiology techniques. Phylum-level analyses revealed a high abundance of Proteobacteria, Acidobacteria, Verrucomicrobia and Actinobacteria, key groups in nutrient recycling, organic matter decomposition and plant-microorganism interaction. In the genus analysis, Nitrospira spp., Candidatus Koribacter spp., Burkholderia spp., Bacillus spp., Flavobacterium spp. and Pedomicrobium spp. were identified, with important functions in nitrification, plant growth promotion, organic matter degradation, and recovery of degraded soils. On the other hand, by using selective and differential media, it was possible to demonstrate the presence of microorganisms such as Enterobacter spp. and Hafnia spp., with the ability to solubilize phosphorus and potassium and produce siderophores, which are likely contributing to the biogeochemical cycles and plant growth within the soil studied. Full article

Neotrinia splendens is widely distributed and is the dominant plant species of temperate degraded grassland in Inner Mongolia, showing a community growing habit forming a ring of individuals. However, there is a lack of attention to the soil microbial communities inside the ring (IN), outside the ring, and under the N. splendens ring (UN). This study investigated the soil bacterial community composition in three different zones of the N. splendens ring using amplicon sequencing technology, as well as soil environmental variables. The soil physicochemical properties, the composition of soil bacterial community, and the soil bacterial α-diversity varied significantly among the three zones. Especially, the growth of N. splendens promotes the soil bacterial diversity in the UN zone due to the interactions between plant and soil microbes. Soil NO₃⁻-N, TC, TN, and pH are the key factors causing the variations of soil bacterial community composition and bacterial diversity. Proteobacteria and Actinobacteria phyla of microorganisms accounted for the largest proportion in network analysis among the three zones. Overall, attention should be paid not only to the improvement of grassland vegetation and soil quality but also to the change in soil microorganisms during the formation and expansion of the N. splendens ring in the future. Full article

Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant’s rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant–microbe interactions and support the development of microbiome-based solutions for salt stress. Full article

Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia’s rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant–root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial–fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability. Full article

At present, there is growing consumer interest in Triticum spelta L., which has high nutritional value. This species is recommended for cultivation in organic farming. In this system of agriculture, biofertilizers are an alternative to mineral fertilization. Biofertilizers stimulate plant growth by providing nutrients through the biological fixation of molecular nitrogen from the air or by increasing the availability of insoluble nutrients in the soil and by synthesizing substances that stimulate plant growth. Green manure biomass and root secretions provide growth material for soil microorganisms, and microorganisms return nutrients to the soil and plants through nutrient decomposition and conversion. Considering the many benefits of using biofertilizers and growing cereals with cover crops for green manure in cereal rotations, field research was carried out on an organic farm to evaluate the soil microbes and the amount of biomass from green manures and their follow-up effect on Triticum spelta L. yields using biofertilizers. Two factors were researched: (I) biofertilizers: control object (no biofertilizer), Azotobacter chroococcum + Azospirillum lipoferum Br 17, Arthrobacter agilis + Bacillus megaterium var. phosphaticum, and combined application of atmospheric nitrogen-fixing bacteria with phosphate solubilizing bacteria; (II) green manures: control object (no green manure application), Trifolium pratense L., Trifolium pratense L. + Lolium multiflorum L., and Lolium multiflorum L. The results show that the most favorable abundance of microorganisms determined in the soil after harvesting Hordeum vulgare L. was recorded after the application of biofertilizers containing atmospheric nitrogen-fixing bacteria with phosphate-solubilizing bacteria under a mixture of Trifolium pratense L. with Lolium multiflorum L. Plowing green manure from a mixture of Trifolium pratense L. with Lolium multiflorum L. resulted in an average increase of 39% in grain yield of Triticum spelta L., while the application of a biofertilizer containing Azotobacter chroococcum + Azospirillum lipoferum Br 17 + Arthrobacter agilis + Bacillus megaterium var. phosphaticum resulted in an average increase of 63%. The proposed spelt wheat cultivation technique can be recommended for agricultural practice due to the positive response of grain yield, but it may also be an important direction for further research to reduce the negative impact of agriculture on the environment. Full article

Rhizosphere microorganisms are crucial for enhancing plant stress resistance. Current studies have shown that Arbuscular mycorrhizal fungi (AMF) can facilitate vegetation recovery in heavy metal-contaminated soils through interactions with rhizosphere microbiota. However, the mechanisms by which AMF influences rhizosphere microbiota and plant growth under cadmium (Cd) stress remain unclear. In this study, Lolium perenne L. was inoculated with AMF (Rhizophagus irregularis) and grown in soils supplemented with Cd (0 mg kg⁻¹, Cd0; 100 mg kg⁻¹, Cd100). Plant biomass, antioxidant enzyme activities, peroxide content, Cd uptake, and rhizosphere bacterial community composition were evaluated. AMF inoculation reduced Cd influx in aboveground tissues, enhanced nutrient availability in the rhizosphere, and mitigated Cd biotoxicity. Additionally, AMF inoculation improved the scavenging efficiency of reactive oxygen species and alleviated oxidative stress in L. perenne, thereby mitigating biomass reduction. Moreover, AMF treatment increased leaf and root biomass by 342.94% and 41.31%, respectively. Furthermore, under the same Cd concentration, AMF inoculation increased bacterial diversity (as measured by the Shannon index) and reduced bacterial enrichment (as indicated by the ACE index). AMF promoted the enrichment of certain bacterial genera (e.g., Proteobacteria and Actinobacteria) in the Cd100 group. These findings suggest that AMF regulated the composition of the rhizosphere bacterial community and promoted the growth of potentially beneficial microorganisms, thereby enhancing the resistance of L. perenne to Cd stress. Cd contamination in soil severely limits plant growth and threatens ecosystem stability, highlighting the need to understand how AMF and rhizosphere microbes can enhance Cd tolerance in L. perenne. Therefore, inoculating plants with AMF is a promising strategy for enhancing their adaptability to Cd-contaminated soils. Full article