Search Results (2,795)

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties of five ecological niches: leaves, fruits, roots, rhizosphere soil, and non-rhizosphere soil. We found that the microbial communities differed significantly between the two varieties. The resistant variety was enriched in beneficial bacteria from the Actinobacteriota phylum and a stable, modular microbial network dominated by saprotrophic fungi. In contrast, the susceptible variety had a higher abundance of opportunistic pathogens and stress-indicator fungi, including Neurospora spp., which were more prominent in the rhizosphere and non-rhizosphere soils. These networks were fragile and dominated by pathotrophic fungi, reflecting ecological imbalance. Our findings show that plant disease resistance is influenced not only by host genetics but also by co-evolutionary interactions with the microbiome. These insights provide a foundation for developing targeted biocontrol strategies to manage plant-associated microbial communities. Full article

Biofilms are complex microbial communities embedded in a self-produced extracellular polymeric matrix. These structures confer increased resistance/tolerance to antimicrobial agents and immune responses, posing a serious challenge in both clinical and industrial contexts. In response to these challenges, increasing attention has been given to the development of novel antibiofilm strategies. Among the promising alternatives are lectins—carbohydrate-binding proteins. This review explores the structural and functional features of biofilms and critically discusses recent studies reporting the antibiofilm effects of lectins. Additionally, it addresses the main challenges and limitations surrounding the practical application of lectins to combat biofilms. Lectins from plants, animals, and microorganisms have shown potential to inhibit biofilm formation by disrupting the extracellular matrix, modulating quorum sensing, and affecting bacterial motility and metabolism. Additionally, they can eradicate established biofilms by degrading the matrix, killing or removing microbial cells, and/or preventing biofilm reformation. Together, the findings reviewed here support the continued investigation of lectins as potential agents against biofilm-associated infections as well as highlight the need to address existing gaps, such as the lack of in vivo studies and limited research on the structure–function relationships of lectins and their antibiofilm activity. Full article

In order to precisely improve the quality of major tree species in northern China, near-natural differentiated management has been gradually introduced into forestry practice, aiming to optimize forest structure, enhance forest quality, and promote nutrient cycling and water conservation. As an essential element of forest ecosystems, soil microbes contribute to biodiversity preservation and nutrient turnover in soils. This study selected three typical forest types (Quercus acutissima forest, Pinus tabulaeformis forest, and Pinus tabulaeformis × Quercus mixed forest) that have been managed with target trees on Zhongtiao Mountain. Using 16S/ITS rRNA high-throughput sequencing, this study systematically assessed the influences of forest type and soil depth (0–60 cm) on the soil properties and microbial communities. The results showed that the fungal alpha diversity indices were the highest in Pinus tabulaeformis forest, which decreased with soil depth. Actinobacteriota exhibited the greatest relative abundance in mixed forest, whereas Ascomycota predominated in the Pinus tabulaeformis forest. The microbial co-occurrence network exhibited greater complexity compared to the pure forest. Microbial carbon and nitrogen cycling functions showed strong correlation with soil pH and nutrient levels. Symbiotrophs dominated the fungal community, and ectomycorrhizae were significantly abundant in mixed forests. pH is the dominant factor driving changes in microbial communities. In summary, the mixed forest improved soil nutrients, enhanced the complexity of microbial networks, and supported higher ectomycorrhizal abundance. These findings provide practical guidance for improving soil health and stability of forest ecosystems through near-natural management. Full article

The mechanisms underlying groundwater microbial community assembly have long attracted attention in earth, environmental, and ecological studies. Nevertheless, limited knowledge is available regarding microbial community assembly within the intact groundwater flow systems in arid regions. In this study, long-term hydrochemical data and microbial community profiles were integrated to unravel the assembly processes and driving forces mediating microbial communities in the Golmud River watershed. Our results indicated that hydrochemical conditions gradually transitioned from oxidizing to reducing environments along the groundwater flow path, as evidenced by a 28.57% and 65.45% decrease in DO and ORP, respectively. Major ions, represented by TDS, displayed minimal variations in phreatic (519.72 ± 16.83 mg/L) and artesian groundwater (486.01 ± 27.71 mg/L), followed by pronounced enrichment in high-salinity groundwater (TDS: 316,112.74 ± 12,452.19 mg/L). Gammaproteobacteria and Actinobacteria declined markedly from phreatic (51.69 ± 6.83% and 9.54 ± 3.40%, respectively) to high-salinity groundwater (13.97 ± 3.70% and 4.77 ± 2.46%). Conversely, halophiles such as Halobacteria and Parcubacteria were rarely detected in low-TDS groundwater, but increased sharply in high-salinity groundwater, reaching 23.22 ± 10.42% and 8.34 ± 3.71%, respectively. Deterministic processes primarily controlled groundwater microbial communities across hydrochemical conditions (relative importance > 50%, NST index < 50%). Microbial co-occurrence networks revealed increasingly tight interactions and intensified competition among communities, driven by accumulated salinity–oxygen stress along the groundwater flow path. This study emphasizes the role of deterministic processes in shaping groundwater microbial community structure, particularly the impact of salinity–oxygen stress. Our findings advance the current understanding of the mechanisms by which hydrochemical processes shape groundwater microbial assemblages. Full article

Enhancing crop productivity through biological strategies is critical for agriculture, particularly under conventional farming systems heavily reliant on chemical inputs. Plant probiotic bacteria offer promising alternatives by promoting plant growth and yield. This is the first field study to assess the effects of biofertilization with native rhizobial strains Rhizobium sp. ACO-34A, Sinorhizobium mexicanum ITTG-R7^T, and S. chiapasense ITTG-S70^T on Solanum lycopersicum (tomato) cultivated under conventional farming conditions. Key parameters assessed include plant performance (plant height, plant stem width, plant dry weight, and chlorophyll content), fruit yield (fruits per plant, fruit height, fruit width, fruit weight, and estimated fruit volume), and macronutrient and micronutrient contents in plant tissue. Additionally, rhizospere bacterial communities were characterized through 16S rRNA amplicon sequencing to evaluate alpha and beta diversity. Inoculation with ITTG-R7^T significantly improved plant height, stem width, and plant dry weight, while ITTG-S70^T enhanced stem width and chlorophyll content. ACO-34A inoculation notably increased fruit number, size, and yield parameters. Moreover, inoculated plants exhibited reduced Fe and Cu accumulation compared to non-inoculated controls. Metagenomic analyses indicated that rhizobial inoculation did not significantly disrupt the native rhizosphere bacterial community. These findings highlight the potential of rhizobial strains as effective plant probiotics that enhance tomato productivity while preserving microbial community structure, supporting the integration of microbial biofertilizers into conventional farming systems. Full article

To evaluate lignite degradation efficiency and the enhancement of biogas production by different microbial treatments, lignite was pre-treated with Streptomyces viridosporus (actinomycete), Phanerochaete chrysosporium (fungus), and Pseudomonas sp. (bacterium), followed by biogasification experiments. Among the three, Phanerochaete chrysosporium exhibited the highest lignite degradation rate. All microbial treatments improved both cumulative biogas yield and methane conversion, with Phanerochaete chrysosporium again demonstrating the most significant enhancement. Ultimate analysis after degradation showed the following consistent trends across all treatments: increases in carbon, hydrogen, and nitrogen contents, and reductions in sulfur and oxygen contents. A linear correlation was observed between the H/C atomic ratio and total biogas yield. Functional group analysis revealed the greatest reductions in key functional groups with Phanerochaete chrysosporium, followed by moderate changes with Pseudomonas and Streptomyces viridosporus. Pore structure characterization indicated that all microorganisms influenced lignite porosity, particularly in mesopore and micropore regions. Increases in pore volume and connectivity were associated with improved biogas production efficiency. Full article

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

Desert ecosystems pose extreme challenges to plant survival. This study explores the adaptive strategies of two xerophytic halophytes, Alhagi sparsifolia and Nitraria roborowskii, in Xinjiang’s Ebinur Lake wetland, focusing on their plant–soil–microbe (PSM) coupling systems across desert gradients. Results revealed significant interspecific and gradient-dependent differences in plant functional traits: A. sparsifolia showed high growth plasticity with a fast-growth strategy, while N. roborowskii adopted a conservative strategy. Rhizosphere soil physicochemical properties and microbial community structure exhibited strong spatial heterogeneity and host specificity, with N. roborowskii having a more complex microbial network and A. sparsifolia showing higher modularity. Multivariate factor analysis elucidated couplings among plant traits, soil properties, enzymes, and microbes. The two species form distinct interaction systems adapted to desert saline–alkali stress, advancing the understanding of ecological adaptation and informing restoration. Full article

Mastitis is a common disease for dairy cows that exerts tremendously detrimental impacts on the productivity of cows and economic viability of pasture. Dihydromyricetin (DMY) is a flavonoid monomeric compound that possesses anti-inflammatory and antioxidant activity. This study aimed at dissecting the effects of DMY on the lactation performance, blood parameters, gut microbiota, and metabolite profiles of dairy cows with subclinical mastitis (SM). The results showed that dietary supplementation with DMY resulted in a reduction in milk somatic cell count, an increase in serum T-AOC and CAT activity, as well as a decrease in serum MDA content. DMY significantly enhanced the prevalence of Coprococcus and Roseburia and reduced the proportion of Cyanobacteria, Proteobacteria, and Dehalobacterium. The amino acid degradation, antibiotic resistance, and O-antigen building blocks biosynthesis (E. coli) capacity of gut microbes were notably diminished by DMY supplementation in cows with SM. Moreover, fecal and plasma metabolomic analysis revealed that DMY intervention reduced the abundance of pro-inflammatory metabolites including arachidonic acid analogues, ω-6 PUFA, and structural components of bacteria. Nevertheless, the levels of anti-inflammatory and antioxidant metabolites involving secondary bile acids, antioxidant vitamins, specific amino acid analogues, etc. were elevated by DMY administration. Overall, DMY might ameliorate SM via enhancing antioxidant capacity and improving the structure of the hindgut microbial community and metabolite profiles in dairy cows. These findings underscore the potential of DMY as a valuable dietary supplement for the improvement of mammary inflammatory diseases in dairy cows. Full article

Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. Of the 350 bats captured using mist nets in Yunnan, nine pregnant Pomona leaf-nosed bats with similar body sizes were chosen. Gut and lung samples were aseptically collected from each bat following cervical dislocation and placed in sterile cryotubes before microbiota investigation. Microbial taxonomic annotation revealed that the phyla Firmicutes and Actinobacteriota were most abundant in the guts of pregnant bats, whereas Proteobacteria and Bacteroidota were abundant in the lungs. Family-level classification revealed that Bacillaceae, Enterobacteriaceae, and Streptococcaceae were more abundant in the guts, whereas Rhizobiaceae and Burkholderiaceae dominated the lungs. Several opportunistic and potentially pathogenic bacterial genera were present at the two body sites. Bacillus, Cronobacter, and Corynebacterium were abundant in the gut, whereas Bartonella, Burkholderia, and Mycoplasma dominated the lungs. Alpha diversity analysis (using Chao1 and Shannon indices) within sample groups examined read depth and species richness, whereas beta diversity using unweighted and weighted UniFrac distance metrics revealed distinct clustering patterns between the two groups. LEfSe analysis revealed significantly enriched bacterial taxa, indicating distinct microbial clusters within the two body sites. The two Random Forest classifiers (MDA and MDG) evaluated the importance of microbial features in the two groups. Comprehensive functional annotation provided insights into the microbiota roles in metabolic activities, human diseases, signal transduction, etc. This study contributes to our understanding of the microbiota structure and functional potential in pregnant wild bats, which may have implications for host physiology, immunity, and the emergence of diseases. Full article

Using meta-analysis of 479 sites across Chinese forests from 136 publications, we quantified changes in soil microbial diversity across forest successional stages and compared patterns between plantation and natural secondary forests. Our systematic review included 136 publications (92 in Chinese, 44 in English), spanning tropical to cold temperate climate zones from 1995–2025. Microbial $\alpha$-diversity exhibited a significant U-shaped pattern across successional stages: early succession (0–15 years) and mature forests (>50 years) had higher Shannon diversity (4.56 ± 0.34 and 4.72 ± 0.41, respectively) than middle-aged forests (16–50 years, 4.18 ± 0.27; standardized mean difference = 0.54, 95% CI: 0.39–0.69, p < 0.01). Response patterns differed significantly among microbial groups (Q = 8.74, p = 0.013), with fungi showing the strongest successional responses (SMD = 0.61, 95% CI: 0.43–0.79), followed by bacteria (SMD = 0.49, 95% CI: 0.32–0.66) and actinomycetes (SMD = 0.42, 95% CI: 0.24–0.60). Natural secondary forests consistently supported higher microbial diversity than plantations (SMD = 0.42, 95% CI: 0.28–0.56), particularly for fungal communities (SMD = 0.47, 95% CI: 0.31–0.63). The climate zone significantly moderated diversity–succession relationships, with subtropical regions showing the largest changes ($\Delta$Shannon = 0.68 ± 0.07) compared to temperate ($\Delta$Shannon = 0.42 ± 0.05) and tropical regions ($\Delta$Shannon = 0.54 ± 0.06). Meta-analytic structural equation modeling revealed that soil organic carbon (path coefficient $\beta$ = 0.68, p < 0.001), total nitrogen ($\beta$ = 0.43, p < 0.001), and pH ($\beta$ = −0.35, p < 0.01) were key mediators connecting succession stage with microbial diversity. Despite substantial between-study heterogeneity (I² = 83.6%), a publication bias was not detected (Egger’s test, p = 0.347). These findings provide the first comprehensive quantification of microbial diversity patterns during forest succession in China, with important implications for forest management and ecological restoration strategies targeting microbial conservation. Full article

Peat soil is a significant global carbon storage pool, accounting for one-third of the global soil carbon pool. Its greenhouse gas emissions have a significant impact on climate change. Seasonal freeze–thaw cycles are common natural phenomena in high-latitude and high-altitude regions. They significantly affect the mineralization of soil organic carbon and greenhouse gas emissions by altering the physical structure, moisture conditions, and microbial communities of the soil. In this study, through the construction of an indoor simulation experiment of the typical freeze–thaw cycle models in spring and autumn in the Greater Xing‘an Range region of China and the Jinchuan peatland of Jilin Longwan National Nature Reserve, the physicochemical properties, greenhouse gas emission fluxes, microbial community structure characteristics, and key metabolic pathways of peat soils in permafrost and seasonally frozen ground areas were determined. The characteristics of greenhouse gas emissions and their influencing mechanisms for peat soil in northern regions under different freeze–thaw conditions were explored. The research found that the freeze–thaw cycle significantly changed the chemical properties of peat soil and significantly affected the emission rates of CO₂, CH₄, and N₂O. It also clarified the interaction relationship between soil’s physicochemical properties (such as dissolved organic carbon (DOC), dissolved organic nitrogen (DON), ammonium nitrogen (NH₄⁺), soil organic carbon (SOC), etc.) and the structure and metabolic function of microbial communities. It is of great significance for accurately assessing the role of peatlands in the global carbon cycle and formulating effective ecological protection and management strategies. Full article

Drought is a global issue that affects agricultural productivity and sustainable development. The application of Bacillus subtilis has significant potential in alleviating drought stress and increasing yield. However, it is not yet clear how Bacillus subtilis affects microbial populations, crop yield, and the biochemical characteristics of rhizosphere soil, as well as the interactions among these factors. In this study, cotton was used as the experimental crop, and different application rates of Bacillus subtilis (0 kg·ha⁻¹ and 45 kg·ha⁻¹ (B)) and drought stress levels (H represents conventional irrigation, 350 mm; L represents 80% of conventional irrigation, 280 mm) were set as three replicates per group. The changes in rhizosphere-soil-related variables, microbial community diversity, enzyme activity, and cotton yield were studied. Compared to the control, the available nitrogen content increased by 19.76–62.40%, and soil moisture increased by 2.48–7.72%. The activities of urease, sucrase, and alkaline phosphatase increased, malondialdehyde content decreased, the Soil Plant Analysis Development (SPAD) value increased, and cotton yield increased by 8.94–9.28%. According to the structural equation model, Bacillus subtilis can increase microbial community diversity and network complexity, improve soil nutrients and enzyme activity, and increase cotton yield. This study’s findings may offer a theoretical foundation for enhancing soil quality and raising agricultural yields in arid regions. Full article

Semi-natural grasslands are key biodiversity reservoirs in Mediterranean mountain ecosystems. Grazing pressure may significantly influence plant communities and soil conditions, with potential effects on ecosystem functioning. This study evaluated the impact of grazing intensity on floristic diversity, community structure, and soil physico-chemical and microbiological properties across eight grasslands in the Jbel Bouhachem massif (northern Morocco). Species richness, Shannon diversity, and floristic composition were assessed using PERMANOVA and NMDS ordination. Soil parameters and microbial groups were analyzed through laboratory measurements, with statistical comparisons based on Wilcoxon and t-tests. No significant differences were found in species richness or alpha diversity between grazing intensities, although floristic dispersion was higher under intensive grazing. Soil texture, potassium, iron, zinc, and electrical conductivity differed significantly between treatments. Among microbial groups, only yeasts and molds showed higher abundance under intensive grazing, while sulfite-reducing clostridia were exclusively detected in these plots. These results suggest that grazing intensity has a selective impact on soil properties and microbial communities, while plant diversity remains relatively stable. Full article

Continuous planting results in a higher occurrence rate of oriental melon Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (FOM), and treatment with Trichoderma can considerably alleviate the incidence of disease. However, the tripartite interaction mechanisms among T. harzianum–melon–rhizosphere microorganisms remain poorly understood in current research. Pot experiments elucidate the growth-promoting, antagonistic, and rhizosphere-regulating effects of T. harzianum on oriental melon. The experiment consisted of two treatments: (1) water control (CK), and (2) T. harzianum inoculation (MM) with three repetitions per treatment. Illumina high-throughput sequencing was employed to analyze the microbial community and associated metabolic pathways. Additionally, a comprehensive correlation analysis clarified how T. harzianum-modulated physiological factors regulate soil microbial communities to enhance melon resistance to FOM. T. harzianum inoculation significantly promoted plant growth, decreased the incidence rate of Fusarium wilt by 41.85%, and increased rhizosphere nitrate-N, pH, EC, and soil enzyme activity (e.g., sucrose and alkaline phosphatase). Notably, T. harzianum inoculation altered the rhizosphere microbial community’s relative abundance and structure, with the most striking changes in the fungal community. Principal coordinate analysis showed this fungal restructuring accounted for 44.9% of total community variation (37% from PCo1, 7.9% from PCo2). Soil-borne pathogens (e.g., Fusarium, Verticillium, Phytophthora) decreased in relative abundance with the inoculation of T. harzianum. Meanwhile, the microbial community shifted from a “fungal-dominated” to “bacterial-dominated” state: fungal proportion decreased by 9.47% (from 23.95% in CK to 14.48% in MM), while bacterial proportion increased by 9.47% (from 76.05% in CK to 85.52% in MM). Microbial abundance shifts primarily impacted amino acid and cofactor biosynthesis metabolic pathways. The application of T. harzianum modified the soil environment, restructuring microbial communities through these changes, which in turn regulated microbial metabolic pathways, creating a soil environment conducive to melon growth and thereby enhancing oriental melon resistance to FOM, while mitigating the obstacles of continuous cropping. Full article