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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

Microbiome analysis has revolutionized our understanding of various biological processes, spanning human health and epidemiology (including antimicrobial resistance and horizontal gene transfer), as well as environmental and agricultural studies. At the heart of microbiome analysis lies the characterization of microbial communities through the quantification of microbial taxa and their dynamics. In the study of bacterial abundances, it is becoming more relevant to consider their relationship, to embed these data in the framework of network theory, allowing characterization of features like node relevance, pathways, and community structure. In this study, we address the primary biases encountered in reconstructing networks through correlation measures, particularly in light of the compositional nature of the data, within-sample diversity, and the presence of a high number of unobserved species. These factors can lead to inaccurate correlation estimates. To tackle these challenges, we employ simulated data to demonstrate how many of these issues can be mitigated by applying typical transformations designed for compositional data. These transformations enable the use of straightforward measures like Pearson’s correlation to correctly identify positive and negative relationships among relative abundances, especially in high-dimensional data, without having any need for further corrections. However, some challenges persist, such as addressing data sparsity, as neglecting this aspect can result in an underestimation of negative correlations. Full article

The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article

In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article

In response to the challenges posed by soil degradation in the arid regions of Xinjiang, China, green and organic management practices have emerged as effective alternatives to conventional agricultural management methods, helping to mitigate soil degradation by promoting natural soil recovery and ecological balance. However, most of the existing studies focus on a single management practice or indicator and lack a systematic assessment of the effects of integrated orchard management in arid zones. This study aims to investigate how different agricultural management practices influence soil physicochemical properties and inter-root microbial communities in apple orchards in Xinjiang and to identify the main physicochemical factors affecting the composition of inter-root microbial communities. Inter-root soil samples were collected from apple orchards under green management (GM), organic management (OM), and conventional management (CM) in major apple-producing regions of Xinjiang. Microbial diversity and community composition of the samples were analyzed using high-throughput amplicon sequencing. The results revealed significant differences (p < 0.05) in soil physicochemical properties across different management practices. Specifically, GM significantly reduced soil pH and C:N compared with OM. Both OM and GM significantly decreased soil available nutrient content compared with CM. Moreover, GM and OM significantly increased bacterial diversity and changed the community composition of bacteria and fungi. Proteobacteria and Ascomycota were identified as the dominant bacteria and fungi, respectively, in all management practices. Linear discriminant analysis (LEfSe) showed that biomarkers were more abundant under OM, suggesting that OM may contribute to ecological functions through specific microbial taxa. Co-occurrence network analysis (building a network of microbial interactions) demonstrated that the topologies of bacteria and fungi varied across different management practices and that OM increased the complexity of microbial co-occurrence networks. Mantel test analysis (analyzing soil factors and microbial community correlations) showed that C:N and available potassium (AK) were significantly and positively correlated with the community composition of bacteria and fungi, and that C:N, soil organic carbon (SOC), and alkaline hydrolyzable nitrogen (AN) were significantly and positively correlated with the diversity of fungi. Redundancy analysis (RDA) further indicated that SOC, C:N, and AK were the primary soil physicochemical factors influencing the composition of microbial communities. This study provides theoretical guidance for the sustainable management of orchards in arid zones. Full article

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

Insects and their bacterial endosymbionts form intricate ecological relationships, yet their role in host–pathogen interactions are not fully elucidated. The small brown planthopper (Laodelphax striatellus), a polyphagous pest of cereal crops, acts as a key vector for rice stripe virus (RSV), a significant threat to rice production. This study aimed to compare the endosymbiont community structures of nonviruliferous and RSV-viruliferous L. striatellus populations using 16S rRNA gene sequencing with high-throughput sequencing technology. Wolbachia was highly dominant in both groups; however, the prevalence of other endosymbionts, specifically Rickettsia and Burkholderia, differed markedly depending on RSV infection. Comprehensive microbial diversity and composition analyses revealed distinct community structures between nonviruliferous and RSV-viruliferous populations, highlighting potential interactions and implications for vector competence and virus transmission dynamics. These findings contribute to understanding virus-insect-endosymbiont dynamics and could inform strategies to mitigate viral spread by targeting symbiotic bacteria. Full article

Straw returning (ST) significantly improves soil quality and profoundly impacts soil microorganisms. However, the effects of different ST application amounts on the soil bacterial community remain unclear, and more studies on optimal ST application amounts are warranted. This study aimed to investigate the bacterial diversity and composition, as well as physicochemical properties, of soil in a corn field with 5-year ST amounts of 0, 3, 4.5, 5, and 6 t/hm², respectively. The results indicated that ST significantly reduced soil bulk density and increased soil pH and nutrients. Meanwhile, ST had a significant effect on the bacterial composition, and the bacterial diversity increased significantly after ST. The relative abundance of Proteobacteria and Acidobacteria increased dramatically, whereas that of Actinobacteria significantly decreased after ST. The amount of ST had threshold effects on soil physicochemical properties and the dominant bacterial phyla. Moreover, the co-occurrence networks indicated that bacterial stability first increased and then decreased with the increase in ST amounts. Soil organic carbon and total nitrogen concentrations were the main drivers of bacterial diversity, whereas soil pH and total nitrogen concentrations were the main drivers of bacterial composition. This study strengthens the fact that ST amounts have threshold effects on the soil physicochemical properties and soil microorganisms, and ST amounts of 3–5 t/hm² were appropriate. Full article

Heavy metal-contaminated soil poses a severe threat to environmental quality and human health, calling for eco-friendly and efficient remediation strategies. This study explored the use of biochar-immobilized copper-resistant Pseudomonas aeruginosa to remediate copper-contaminated soil and promote growth of Chinese milk vetch (Astragalus sinicus L.). Indoor pot experiments compared four groups: copper-contaminated soil (control), soil with biochar, soil with free bacteria, and soil with biochar-immobilized bacteria (IM). Results showed IM had the most significant effects on soil properties: it raised pH to 7.04, reduced bioavailable copper by 34.37%, and increased catalase (3.48%) and urease (78.95%) activities. IM also altered soil bacterial communities, decreasing their richness and evenness (alpha diversity) while shifting community composition. For Chinese milk vetch, IM reduced leaf malondialdehyde (a marker of oxidative stress) by 15%, increased total dry weight by 90%, and lowered copper accumulation in roots (18.62%) and shoots (60.33%). As a nitrogen-fixing plant, the vetch’s nitrogen fixation in roots and shoots rose by 82.70% and 57.08%, respectively, under IM. These findings demonstrate that biochar-immobilized Pseudomonas aeruginosa is a promising in situ amendment for remediating copper-contaminated soil and boosting plant growth. Full article

This study aims to analyze the differences in soil bacterial community structure under different vegetation restoration types, and to explore the role of microorganisms in the process of vegetation restoration on the soil ecosystem of the Grain for Green area in the Loess Plateau. High-throughput sequencing technology was used to analyze the alpha diversity of soil bacteria, community structure characteristics, and the correlation between soil environmental factors and bacterial communities in different artificial Hippophae rhamnoides forests. Soil microbial C and N show a decreasing trend with an increase in the 0–100 cm soil layers. The results indicated that the bacterial communities comprised 24 phyla, 55 classes, 110 orders, 206 families, 348 genera, 680 species, and 1989 OTUs. Additionally, the richness indices and diversity indices of the bacterial community in arbor shrub mixed forest are higher than those in shrub pure forest, and the indices of shrub forest on sunny slope are higher than those on shady slope. Across all samples, the dominant groups were Actinobacteria (37.27% on average), followed by Proteobacteria (23.91%), Acidobacteria (12.75%), and Chloroflexi (12.27%). Soil nutrient supply, such as TOC, TN, AN, AP, and AK, had crucial roles in shaping the composition and diversity of the bacterial communities. The findings reveal that vegetation restoration significantly affected soil bacterial community richness and diversity. Furthermore, based on the results, our data provide a starting point for establishing soil bacterial databases in the Loess Plateau, as well as for the plants associated with the vegetation restoration. Full article

Stipagrostis pennata is an important plant in desert ecosystems. Its seed-endophytic bacteria may play a critical role in plant growth and environmental adaptation processes. This study systematically analyzed the community composition and potential plant growth-promoting (PGP) functions of seed-endophytic bacteria associated with S. pennata. The results showed that while the overall diversity of bacterial communities from different sampling sites was similar, significant differences were observed in specific functional genes and species abundances. Nine endophytic bacterial strains were isolated from the seeds, among which Bacillus altitudinis strain L7 exhibited phosphorus solubilizing capabilities, nitrogen fixing, IAA production, siderophore generation, and multi-hydrolytic enzyme activities. Additionally, the genomic sequencing of L7 revealed the key genes involved in plant growth promotion and environmental adaptation, including Na⁺ efflux systems, K⁺ transport systems, compatible solute synthesis genes, and the gene clusters associated with nitrogen metabolism, IAA synthesis, phosphate solubilization, and siderophore synthesis. Strain L7 exhibits salt and osmotic stress tolerance while promoting plant growth, providing a promising candidate for desert microbial resource utilization and plant biostimulant development. Full article

To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article

The Qinghai–Tibet Plateau, a region susceptible to global change, stores substantial amounts of soil organic carbon (SOC) in its alpine grassland. However, little is known about how SOC is regulated by soil microbial communities, which vary with elevation, mean annual temperature (MAT), and mean annual precipitation (MAP). This study integrates phospholipid fatty acid (PLFA) analysis to simultaneously resolve microbial biomass, community composition, and membrane lipid adaptations along an elevational gradient (2861–5090 m) on the Qinghai–Tibet Plateau. This study found that microbial PLFAs increased significantly with rising MAP, while the relationship with MAT was nonlinear. PLFAs of different microbial groups all had a positive effect on SOC storage. At higher altitudes (characterized by lower MAP and lower MAT), Gram-positive bacteria dominated bacterial communities, and fungi dominated the overall microbial community, highlighting microbial structural adaptations as key regulators of carbon storage. Saturated fatty acids with branches of soil microbial membrane dominated across sites, but their prevalence over unsaturated fatty acids decreased at high elevations. These findings establish a mechanistic link between climate-driven microbial community restructuring and SOC vulnerability on the QTP, providing a predictive framework for carbon–climate feedbacks in alpine systems under global warming. Full article

L-carnitine and Mildronate are substances that can significantly rearrange the energy metabolism of cells. This can potentially cause changes in the bacterial composition of the gut microbiome and affect testis functionality and male sexual health. Mice of the C57Bl/6 line were used. Sexual behavior was assessed using physiological tests, and gene expression patterns were assessed by qPCR. High-throughput sequencing of mouse fecal microbiota was performed. We showed that long-term administration of Mildronate has no significant effect on the intestinal microbiome, and there was a compensatory increase in the expression of genes involved in fatty acid and leptin metabolism. No impairment of sexual motivation in male mice was observed. Prolonged L-carnitine supplementation caused a decrease in alpha diversity of bacteria and a decrease in some groups of microorganisms that are components of a healthy gut microflora. A correlation was observed between the level of bacteria from Firmicutes phylum, indicators of sexual motivation of mice, and the dynamics of body weight gain. Our results may indicate that metabolic modulators can have a significant impact on the structure of the bacterial community of the gut microbiome, which may influence male sexual health through the gut–semen axis. Full article

This study aims to evaluate the effect of adding a chitosan/perlite (Ch/P) carrier to anaerobic digestion (AD) on the efficiency and kinetics of the process, as well as the directional changes in the bacterial microbiome. A carrier with this composition was applied in the AD process for the first time. A laboratory experiment using wafer waste (WF) and cheese (CE) waste was conducted under mesophilic conditions. The analysis of physico-chemical properties confirmed the suitability of the tested carrier material for anaerobic digestion. Both components influenced the microstructural characteristics of the carrier: perlite contributed to the development of specific surface area, while chitosan determined the porosity of the system. Using next-generation sequencing (NGS), the study examined how the additive affected the genetic diversity of bacterial communities. Fourier-transform infrared spectroscopy (FTIR) revealed that the degradation rate depended on both the carrier and the substrate type. Consequently, the presence of the carrier led to an increase in the volume of biogas and methane produced. The volume of methane for the wafer waste (WF–control) increased from 351.72 m³ Mg⁻¹ (VS) to 410.74 m³ Mg⁻¹ (VS), while for the cosubstrate sample (wafer and cheese, WFC–control), it increased from 476.84 m³ Mg⁻¹ (VS) to 588.55 m³ Mg⁻¹ (VS). Full article