Search Results (1,591)

Calcareous soils are typically deficient in essential nutrients such as iron, phosphorus, and potassium, which frequently results in nutrient deficiency in fruit trees. Bacillus licheniformis LCDD6 markedly enhanced Malus hupehensis seedling growth and plant iron nutrition in calcareous soil. This study aimed to elucidate the mechanism underlying these beneficial effects of strain LCDD6 under iron deficiency. Transcriptomic analysis revealed that iron deficiency induced metabolic reprogramming in strain LCDD6, characterized by a significant upregulation of genes involved in the biosynthesis of the siderophore bacillibactin and plant growth hormone indoleacetic acid (IAA). Consistently, metabolomic profiling identified bacillibactin and IAA as the dominant metabolites produced under iron-deficient conditions. A 60-day pot experiment further demonstrated that the cell-free fermentation broth of strain LCDD6 significantly enhanced plant growth and rhizosphere soil enzyme activities. The crude bacillibactin extract derived from the fermentation exerted the strongest effects on plant growth and iron accumulation, whereas IAA preferentially stimulated root development and promoted plant phosphorus accumulation. Additionally, different metabolites exerted distinct and selective effects on the rhizosphere microbial community, with fungi showing stronger and more metabolite-specific responses than bacteria. The crude bacillibactin extract enriched fungal taxa, particularly Coprinellus, which showed strong positive correlations with plant growth traits and iron accumulation, while Stachybotrys, enriched under IAA treatment, was positively correlated with plant phosphorus content. Overall, strain LCDD6 promotes plant growth under iron-deficient conditions through the coordinated action of multiple metabolites, with bacillibactin as the primary contributor and IAA providing complementary effects. These findings offer mechanistic insight and a scientific basis for developing Bacillus-based biofertilizers to improve nutrient acquisition in calcareous soils. Full article

Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen (N) essential for plant growth. While rhizobia remain the central actors in this symbiosis, recent discoveries reveal the presence of non-rhizobial endophytes within nodules, suggesting a complex interplay shaped by host selection and compatibility with rhizobial partners. Understanding the structure and dynamics of crop nodule-associated microbial communities is thus critical for optimizing host responses to rhizobia and for leveraging beneficial plant–microbe interactions. This review explores the dualistic nature—both facilitative and inhibitory—of the nodule microbiome in relation to nodulation. We examine the diversity of soil bacteria that stimulate nodulation and those that ultimately colonize nodule tissues, questioning whether these functional groups overlap. Furthermore, we discuss the molecular dialogs and counter-signaling mechanisms that regulate endophyte ingress into nodules, and evaluate how nodule endophytes contribute to plant performance and soil fertility. Full article

In nature, a significant number of plant species form symbiotic associations with microorganisms, with arbuscular mycorrhizal fungi (AMF) and endophytic fungi being two prevalent groups of these partners. However, the ability to establish such symbioses with AMF and endophytic fungi is limited to a small fraction of native grass species. Nitrogen is a crucial nutrient for plant growth, yet it is often a limiting factor, underscoring the importance of understanding how plants acquire it. AMF enhance plant growth by improving nitrogen uptake efficiency, but the combined effects of endophytic fungi and AMF on plant physiology and ecology remain underexplored. To address this knowledge gap, in the present study, we conducted an indoor randomized block experiment to investigate the influence of endophytic fungi and AMF infection on the physiological and ecological attributes of Festuca rubra under various nitrogen regimes. The findings indicated that AMF inoculation significantly affected the total carbon content of F. rubra and the total sulfur concentration in its underground tissues across different nitrogen conditions. Additionally, dual colonization by AMF and endophytic fungi had a significant impact on the underground total nitrogen content of the plants. Furthermore, the complex interactions among AMF, endophytic fungi, and nitrogen availability emerged as critical determinants influencing underground total carbon content, transpiration rates, intercellular carbon dioxide concentrations, and the activity of soil extracellular enzymes in F. rubra. The activity of soil extracellular enzymes and pH significantly affected the structure and diversity of rhizosphere bacterial, fungal, and archaeal communities. AMF enhanced the richness of rhizosphere bacterial communities under low-nitrogen conditions, whereas endophytic fungi infection increased bacterial diversity. Soil extracellular enzyme activity and pH were closely related to the community structures and diversities of rhizosphere bacteria, fungi, and archaea. This study clarifies the effects of AMF and endophytic fungi infection on the physiological and ecological characteristics of F. rubra, significantly contributing to our understanding of the synergistic mechanisms governing the interactions among AMF, endophytic fungi, and their host plants. Full article

Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from “sensitive” to “tolerant” microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC₅₀ values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L⁻¹) were significantly higher than those for pathogens (1.3–7.9 mg/L). This study established a microbial “sensitive-tolerant” response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils. Full article

Hydrocarbon-based rocket fuels, particularly kerosene grades T-1 and RG-1 used during launch vehicle operations, represent a persistent source of soil contamination in areas impacted by rocket stages. This study quantitatively evaluates the response and recovery dynamics of soil microbial communities in Calcisol (Loamic) soils from the U-25 impact area near the “Baikonur” Cosmodrome (Kazakhstan) under controlled kerosene contamination. Eleven soil samples were monitored over 90 days, including one uncontaminated control and ten samples exposed to increasing concentrations of T-1 or RG-1 (100–15,000 mg/kg). Microbial indicators included total microbial count, actinomycetes, microscopic fungi, and spore-forming bacteria, expressed as CFU/g (mean ± SD, n = 3). Acute exposure caused significant reductions in total microbial abundance (28–58%) and microscopic fungi (43–75%, p ≤ 0.05), indicating pronounced short-term toxicity. By Day 90, bacterial and actinomycete populations exhibited partial to complete recovery, with some treatments exceeding control values, suggesting metabolic adaptation and hydrocarbon utilization. In contrast, fungal populations remained consistently suppressed throughout the experiment, indicating prolonged ecological stress. No strict dose–response relationship was observed, highlighting the influence of soil physicochemical properties on microbial resilience and hydrocarbon bioavailability. These findings identify microscopic fungi as the most sensitive indicators of kerosene contamination, suggesting that indigenous bacterial and actinomycete communities play a key role in natural attenuation. The results provide quantitative thresholds relevant for environmental monitoring and support the development of microbiologically informed bioremediation strategies in areas impacted by rocket launches. Full article

Comfrey (Symphytum officinale L.) was a promising crop in the integrated crop–livestock pattern. However, the impact of long-term irrigation with treated poultry wastewater (TPW) on soil chemical properties and bacterial community, as well as the contribution of comfrey to mitigate N accumulation in soil, remain unclear. This study investigated the changes in chemical and microbiological characteristics of the comfrey soil under six-year TPW irrigation (grassland) in comparison with the adjacent conventional crop soil irrigated with freshwater (farmland). Results showed that N accumulation in comfrey accounted for 66.0% of the N input from TPW irrigation. In grassland, soil pH at all depths increased by one unit and EC in the subsoil increased by 33.5–42.4%, while TN and NO₃⁻-N in the surface soil decreased by 26.7% and 64.5%, respectively. The composition and structure of the bacterial community in the grassland dramatically changed, and the relative abundances of nitrite-oxidizing bacteria Nitrospira and ammonifying bacterium Flavobacterium and Pseudomonas increased by 0.1–3.6-, 3.8–11.0- and 0.1–6.0-fold, respectively, while those of saline-alkali-sensitive bacteria Sphingomonas decreased by 72.3–83.2% in the subsoil. Soil pH and NO₃⁻-N were the primary factors influencing changes in bacterial communities. These findings revealed that there was no nitrogen accumulation, but alkalization occurred in the comfrey field under long-term TPW irrigation, which highlighted the prospective application of comfrey in the crop–livestock system. Full article

Rapid urbanization threatens soil biodiversity and ecosystem functions, but the structural and physiological adaptations of soil microorganisms to urbanization remain unclear. We examined variations in soil microbial biomass, community structure and membrane lipid composition along an urban–suburban–exurban gradient in Guangzhou, China, using phospholipid fatty acid analysis. Samples were collected from four to five quadrats per site at three depths during dry and wet seasons. PERMANOVA revealed that both the urbanization gradient and the soil depth significantly shaped microbial communities. Depth was the strongest driver, explaining 45.5% of the variance in total microbial biomass, while site explained 27.2%. Microbial biomass decreased from exurban to urban sites and from surface to deep soils. Concurrently, the ratios of fungi/bacteria and Gram-positive/Gram-negative bacteria increased in urban areas and deeper soils. Physiologically, the membrane lipids shifted toward more saturated fatty acids in urban and surface soils, while unsaturated fatty acids predominated in exurban and deeper layers. These shifts in microbial community structure and membrane lipid composition were strongly correlated with key soil properties, including soil organic carbon, total nitrogen, and bulk density. The findings demonstrate urbanization diminishes microbial biomass and triggers adaptive microbial responses, providing a scientific basis for the sustainable management of urban forests. Full article

As a fast-growing timber tree species with a wide cultivation area, poplar is facing the problem of declining economic benefits under long-term monoculture. Intercropping provides an effective solution. Using Illumina Miseq sequencing, we analyzed soil microbiomes under four patterns: poplar monoculture, and intercropping with amorpha fruticosa, black locust, or cassia seed. The results showed that the Alpha diversity index of intercropping area was significantly higher than that of single planting poplar area under intercropping and monoculture conditions. In the intercropping area, the highest species richness was the intercropping of poplar and black locust, and the lowest was the intercropping of poplar and amorpha fruticosa. The dominant microorganisms in the intercropping mode were Vicinamibacterales, and the fungi were Alternaia and Enterocarpus. In the single planting poplar area, a large number of bacteria gathered in the soil were Dongia and Alphaproteobacteria, and fungi were Fusarium and Mortierella. Functional prediction results showed that the biosynthetic function of ansamycin was the highest in the bacterial community. In the intercropping area, the functional abundance of methanol oxidation, sulfate respiration, sulfate compound respiration, nitrate denitrification, nitrite denitrification, and nitrous oxide denitrification was higher than that in the single planting poplar area. On the contrary, the abundance of methanotrophy function is lower than that of single planting poplar area. In the fungal community, the functional abundance of animal pathogens and the animal pathogen–dung saprotroph–endophyte–plant saprotroph–soil saprotroph–wood saprotroph group in the monoculture poplar area was higher than that in the three intercropping areas. In summary, the intercropping mode of poplar is better than the monoculture mode, and the species richness is the highest when poplar and black locust are intercropped. Therefore, the intercropping pattern of poplar and other tree species improved microbial community. This provides some theoretical guidance for the subsequent solution of continuous cropping obstacles in poplar. Full article

To investigate the effects of mixed forests on soil bacterial characteristics in the Yellow River Delta, pure forests of Ailanthus altissima, Ulmus pumila, Robinia pseudoacacia, and Fraxinus velutina (hereafter Aa, Up, Rp, and Fv, respectively) and mixed forests of Aa-Rp, Up-Rp, Fv-Rp, and Ma (Melia azedarach)-Fv were selected as the research objects. High-throughput sequencing technology was employed to analyze the structure, diversity, and function of bacterial communities in this region. The results showed that Acidobacteria, Proteobacteria, and Actinobacteria were the dominant microbial groups. The relative abundance of Acidobacteria was reduced by mixed patterns of Up-Rp, Fv-Rp and Ma-Fv, and the abundance of Proteobacteria was increased in Ma-Fv. The Chao1, ACE and Shannon indices of Aa-Rp and Fv-Rp were increased, while the Chao1 and ACE indices of Up-Rp and Ma-Fv were decreased. Functional prediction revealed that chemoheterotrophic and aerobic chemoheterotrophic bacteria had the highest abundance, with mixed forests exerting variable effects on different functional bacterial groups. In conclusion, mixed forest management exerts a significant influence on shaping bacterial community structure, regulating its diversity, and facilitating the directional enrichment of functional bacteria, which is conducive to enhancing the stability and sustainability of plantations. Full article

Olive orchard soils are a source of microorganisms capable of inhibiting major olive pathogens. In this study, rhizobacteria were isolated and characterized based on plant growth-promoting traits, and soil 16 rRNA gene sequencing analysis was performed to analyze microbial communities at two key olive phenological stages (flowering and fruit formation). Using a culture-dependent approach, a total of 90 bacterial isolates representing distinct colony morphotypes were recovered from olive soils, with 35 during the flowering stage and 55 during the fruit formation stage, indicating a higher cultivable diversity during the latter period. We identified some bacterial strains with antagonistic activity and observed phenology-related shifts in the soil microbiome. Using differential abundance analysis, we identified bacterial taxa that were significantly enriched or depleted during olive fruit formation. Overall, this study demonstrates that olive-associated bacteria harbor antagonistic potential against olive pathogens. The use of bacteria adapted to olive agroecosystems represents a promising strategy for sustainable disease management. Full article

Soil microorganisms are important components of forest ecosystems and play a key role in biogeochemical cycling. Bamboo is invasive due to its strong clonal expansion ability, which often leads to changes in plant communities and soil environments, thus affecting soil microorganisms. However, the existing research focuses on the response of moso bamboo (Phyllostachys edulis) and soil fungi and bacteria, and little attention is paid to other bamboo species and their impact on soil protists. In this study, we examined the effects of Bambusa emeiensis expansion on the soil microbial communities in subtropical evergreen broad-leaved forests. B. emeiensis expansion significantly reduced plant diversity and soil pH (p < 0.05). The expansion of B. emeiensis did not significantly change the relative abundance of dominant bacteria and fungi groups in the soil, but significantly changed the community composition of protists, including a significant increase in the relative abundance of Cercozoa, while the Evosea_X group and Ciliophora decreased significantly (p < 0.05). While α-diversity remained unchanged across all microbial groups, only protist community structure differed significantly (p = 0.026). The main driver of protist variation was identified as plant diversity decline by redundancy analysis (R² = 0.760, p = 0.032). These results can be interpreted within a bottom-up regulatory framework, in which plant diversity is linked to changes in protist community composition. Overall, protists are an important group of organisms that help us understand the impact of bamboo growth on the environment. Their role in nutrient cycling and soil fertility suggests that changes in protist communities may have broader implications for ecosystem sustainability. This study provides a scientific reference for the ecological management of regional B. emeiensis and highlights the potential impact of protist community shifts on soil health and ecosystem resilience. Full article

This study investigated the effects of bio-organic fertilizer (BF) containing plant growth-promoting bacterium Bacillus velezensis SS-20 on soil properties, microbial community structure, and C/N cycle functional genes. The results showed that compared with chemical fertilizer (CF) and deactivated bio-organic fertilizer (BFD) treatments, BF significantly improved soil physicochemical properties. Soil pH, organic matter, total nitrogen, total potassium, and total phosphorus content under BF treatment were increased by 14.8%, 56.5%, 48.2%, 38.8%, and 58.4%, respectively, compared to the control; soil urease and sucrase activities increased by 3.5 and 2.4 times those of CF treatment, respectively. Meanwhile, BF increased pakchoi yield by 11.2% (vs. CF). BF treatment enhanced the relative abundance of beneficial bacteria Actinomycetota by 28.4% compared with the BFD treatment and raised that of fungi Ascomycota to 1.9 times that of the control. At the genus level, BF significantly enriched biocontrol-relevant genus Pseudogymnoascus, whose abundance reached three times that of CF treatment, while the abundance of potentially harmful genus Penicillium decreased by 82%. BF also led to a high degree of synergy in carbon and nitrogen cycles. Functional gene analysis indicated that BF down-regulated multiple carbon-degrading genes, increased organic nitrogen metabolism genes by 5.3%, and reduced denitrification genes by 13.3%. Overall, bio-organic fertilizer optimized the soil microenvironment, regulated the microbial community structure, and improved C/N use efficiency and plant growth by introducing functional microorganisms and organic matter. Full article

Microplastics (MPs) can serve as bearers of microorganisms and additional contaminants. However, the functional composition and assembly processes of plastisphere bacteria in co-contaminated soil–plant systems are not yet well understood. Using a pot experiment, we examined the effects of both individual and combined cadmium (Cd) and polypropylene (PP) MP contamination on the development of the bioenergy plant sorghum. The bacterial community, co-occurrence networks, and assembly processes in the rhizosphere soil and PP plastisphere were investigated using high-throughput sequencing. Compared with contamination by a single compound, combined contamination with Cd and PP had a more potent inhibitory effect on the development of sorghum. PCoA and diversity indices indicate that the bacterial community on PP plastics is structurally simpler than that in rhizosphere soil. The PP plastisphere could recruit bacteria from the genera Sphingomonas, Rhizobium, and Bacillus. The bacterial communities in the soil and the PP plastisphere were mostly formed by stochastic processes, with diffusion limitation playing a greater role in the bacterial community in the PP plastisphere. Co-occurrence network analysis revealed differences between the bacterial communities in the soil and in the PP plastisphere, with the network in the PP plastisphere showing lower complexity and connectivity. Functional prediction revealed that the prevalence of nitrogen cycling genes was greater in the PP plastisphere than in the dirt and that the PP plastisphere presented greater metabolic activity. The relative prevalence of metabolic pathways associated with human diseases was markedly elevated in the PP plastisphere, which may be correlated with the dissemination of pathogenic microorganisms. These findings indicate that the PP plastisphere, as a distinct microbial niche, might attract certain bacteria, consequently affecting the functional characteristics of cocontaminated soil–plant systems. Full article

In severely saline-alkali soils, surface salt accumulation caused by intense water evaporation results in elevated salinity, low organic matter content, and suppressed microbial activity, collectively impairing plant physiological metabolism and growth. Superabsorbent polymers hold significant potential for ameliorating saline-alkali soils by regulating soil water–salt dynamics. Biochar, a carbon-rich organic material, plays a pivotal role in enhancing soil organic matter storage, whereas vermicompost, a microbiologically active organic amendment, contributes substantially to improving soil microbial functions. Therefore, this study developed a novel superabsorbent polymer reinforced with vermicompost and biochar (VB-SAP) and further investigated its effects on metabolic pathways associated with enhanced S. cannabina stress resistance in severely saline-alkali soils. The results showed that VB-SAPs significantly increased soil water and organic matter contents by 10.9% and 38.7% (p < 0.05), respectively, and decreased topsoil salinity of saline soils by 44.9% (p < 0.05). The application of VB-SAP altered the soil bacterial community structure and increased the complexity of the bacterial co-occurrence network, specifically enriching members of the phylum Pseudomonadota, which are widely recognized as common plant growth-promoting rhizobacteria. Moreover, VB-SAPs significantly upregulated root-associated salt tolerance genes involved in phenylpropanoid biosynthesis, tryptophan metabolism, and arginine–proline pathways, thereby enhancing root biomass accumulation, nutrient uptake, and shoot growth of S. cannabina. Collectively, these findings reveal that the new type of superabsorbent polymer reinforced with vermicompost and biochar may enhance the salt tolerance and growth of S. cannabina by reshaping the rhizosphere microenvironment, including reducing soil salinity, increasing soil water and organic matter contents, and promoting beneficial bacteria in severely saline-alkali soil, thereby providing novel strategies for the integrated improvement of saline soils. Full article

Artificial cyanobacterial crusts (ACCs) are a potentially effective biological strategy for combating desertification. However, while functional microorganisms influence ACCs formation efficiency, research on their role is limited, and their underlying promotion mechanisms remain unclear. Here, we investigated the effects of three functional synthetic microbial communities (SynComs), each dominated by microorganisms specialized in exopolysaccharide (EPS) production (3 strains), siderophore production (3 strains), or nitrogen fixation (4 strains), on ACCs formation following inoculation with Microcoleus vaginatus. This study was carried out in a controlled laboratory setting with a 12 h light/dark cycle and a light intensity of 2400–2700 lux. Following a 24-day cultivation period, EPS-producing or nitrogen-fixing SynComs significantly increased the chlorophyll-a content by 16.0–16.3%. Except for the nitrogen-fixing bacteria treatment, other SynComs enhanced the soil organic matter content of ACCs by 9.1% to 27.3%. The content of EPS was significantly improved by all three SynComs by 14.1~19.2%. Urease activity rose by 6.7% when siderophore-producing bacteria were added. The impacts of SynComs on ammonium nitrogen (NH₄⁺-N) showed different temporal dynamics: nitrogen-fixing SynComs significantly increased NH₄⁺-N early (≤10 days), while EPS-producing and siderophore-producing SynComs enhanced accumulation later (17–24 days). SynComs inoculation markedly accelerated cyanobacterial and general microbial colonization and growth. In comparison to day 0, the 16S rRNA gene copy number of ACCs increased by 24.1% and 43.0%, respectively, in the EPS-producing and nitrogen-fixing SynComs. Additionally, correlation analysis showed that SynComs transformed the weak correlations in the control into a strong positive correlation between NH₄⁺-N and both Chl-a and microbial biomass. Our findings demonstrate SynComs, particularly the EPS-producing or nitrogen-fixing SynComs, enhance ACCs formation through elucidated mechanisms, providing a theoretical basis for optimizing ACCs-based desertification control strategies. Full article