Search Results (289)

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

Organic farming is widely recognized as a promising practice for sustainable agriculture, yet its long-term ecological impacts remain insufficiently investigated. In this study, we evaluated these impacts by comparing heavy metal concentrations, soil invertebrate communities, and microbial profiles between long-term organic and conventional farming systems. A comparative analysis was conducted on 24 plot soils from two paired organic and conventional farm systems in Beijing, each managed continuously for over 20 years. Our results revealed that soils under organic management consistently contained 10.8% to 73.7% lower heavy metals, along with reduced geo-accumulation indices (I_geo, a standardized metric for soil contamination assessment), indicating decreased contamination risks. In terms of soil fauna, while conventional soils showed higher Collembola abundance, organic farming significantly enhanced Collembola richness and diversity by 20.6% to 55.0%. Microbial sequencing likewise revealed enhanced richness and diversity of bacteria and fungi in organic soils. These microbial communities also displayed shifts in dominant taxa and more stable co-occurrence networks under organic management. Principal component analysis and Mantel tests identified soil pH and nutrients as key drivers of soil biodiversity, while heavy metals also imposed negative influences. Collectively, these findings demonstrate that long-term organic farming not only mitigates environmental risks associated with soil contaminants but also promotes belowground ecological integrity by supporting biodiversity of soil fauna and microbiota. This study highlights the ecological significance of sustained organic practices and provides critical insights for advancing sustainable agricultural developments. Full article

Microbial communities are crucial to maintaining the ecological health of lakes, but their response to water quality and eutrophication is poorly understood. This study analyzed seasonal variation in the effect of water quality parameters on microbial community structure and function at southern Lake Taihu. We observed poor water quality in autumn (low dissolved oxygen concentration and water transparency) with severe eutrophication (high in nitrogen, phosphorus, and microcystins). Microcystins were a major indicator of water quality that affected total phosphorus and dissolved oxygen concentrations. Redundancy analysis revealed that total nitrogen, total phosphorus, nitrate, ammonium, and microcystins, temperature, and dissolved oxygen all significantly influenced the microbial community. Microbial co-occurrence networks revealed significant seasonal variations, with autumn and winter exhibiting a more complex structure than other seasons. Additionally, we identified microcystin-sensitive microbial species as eutrophication indicators; they are involved in bacterial community components and metabolic function and fluctuate under seasonal changes to water quality. In conclusion, our findings provide insight into the relationship between water quality and microbial communities, offering an empirical basis for improving the sustainable management of Lake Taihu. Full article

Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (p < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (p < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure. Full article

Background/Objective: Oral lichen planus (OLP) is a chronic inflammatory disorder of the oral mucosa with unclear etiology. Increasing evidence implicates oral microbial dysbiosis in its pathogenesis, but little is known about supragingival plaque communities in relation to clinical subtypes. This cross-sectional case–control study aimed to characterize the supragingival plaque microbiota and microbial interaction networks in erosive OLP (E-OLP), non-erosive OLP (NE-OLP), and healthy controls (HCs), to elucidate microbial patterns associated with disease severity. Methods: Supragingival plaque samples were collected from 90 participants (30 per group) and analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance, and co-occurrence network analyses were performed. Results: E-OLP exhibited pronounced dysbiosis, including the enrichment of pro-inflammatory taxa (e.g., Prevotella, Parvimonas) and depletion of health-associated commensals (e.g., Rothia, Capnocytophaga). Network analysis revealed the stepwise disintegration of microbial community structure from HC to NE-OLP to E-OLP, with reduced connectivity and increased dominance of pathogenic clusters in E-OLP. These microbial alterations aligned with clinical findings, as E-OLP patients showed significantly higher Reticulation/keratosis, Erythema, and Ulceration (REU) scores for erythema and ulceration compared to NE-OLP. Conclusions: Supragingival plaque dysbiosis and ecological disruption are strongly associated with OLP severity and subtype. This study highlights the utility of plaque-based microbial profiling in capturing lesion-proximal dysbiotic signals, which may complement mucosal and salivary analyses in future diagnostic frameworks. Multi-omics approaches incorporating fungal, viral, and metabolic profiling are warranted to fully elucidate host–microbe interactions in OLP. Full article

This study aims to reveal the impact mechanisms of five typical topographic habitats in the Sanjiangyuan region (sunny slope, depression, shady slope, mountain pass, and transitional zone) on the characteristics and functions of rhizosphere soil fungal communities of Kengyilia thoroldiana, and to elucidate the association patterns between these communities and soil physicochemical factors. The species composition, diversity, molecular co-occurrence network, and FUNGuild function of microbial communities were investigated based on high-throughput sequencing technology. By combining the Mantel test and RDA analysis, the key habitat factors affecting the structure of the soil fungal community in the rhizosphere zone of Kengyilia thoroldiana were explored. The results showed that: ① The composition of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographical habitats showed significant differentiation characteristics: the number of OTUs in H2 (depression) and H5 (transitional zone) habitats was the highest (336 and 326, respectively). Habitats H2 showed a significant increase in the abundance of Ascomycota and Mortierellomycota and a significant decrease in the abundance of Basidiomycota compared to the other topographical habitats. ② The diversity and aggregation degree of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographical habitats showed differences. ③ Cluster analysis showed that the rhizosphere soil fungi in five topographical habitats of Kengyilia thoroldiana could be divided into two groups, with H2, H4 (mountain pass), and H5 habitats as one group (group 1) and H1 and H3 (shady slope) as one group (group 2). ④ The characteristics of the Kengyilia thoroldiana community and the physical and chemical properties of rhizosphere soil in five topographical habitats were significantly different, and the height, coverage, biomass, and soil nutrient content were the highest in H2 and H5 habitats, while lower in H1 and H3 habitats, with significant differences (p < 0.05). ⑤ Redundancy analysis showed that soil water content was the main driving factor to change the structure and function of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographic habitats in the Sanjiangyuan region. This study demonstrated that topographic habitats affected the species composition, functional pattern, and ecosystem service efficiency of the Kengyilia thoroldiana rhizosphere fungal community by mediating soil environmental heterogeneity, which provides microbial mechanistic insights for alpine meadow ecosystem protection. Full article

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

The coastal zone presents complex hydrodynamic interactions among inland groundwater, reservoir water, and intruding seawater, with important implications for ecosystem functioning and water quality. However, the relative roles of hydraulic connectivity and seawater-driven salinity gradients in shaping microbial communities at the aquifer–reservoir interface remain unclear. Here, we integrated hydrochemical analyses with high-throughput 16S rRNA gene sequencing to investigate bacterial community composition, assembly processes, and co-occurrence network patterns across groundwater_in (entering the reservoir), groundwater_out (exiting the reservoir), and reservoir water in a coastal system. Our findings reveal that seawater intrusion exerts a stronger influence on groundwater_out, leading to distinct chemical profiles and salinity-driven environmental filtering, whereas hydraulic connectivity promotes greater microbial similarity between groundwater_in and reservoir water. Groundwater samples exhibited higher alpha and beta diversity compared to the reservoir, with dominant taxa such as Comamonadaceae, Flavobacteriaceae, and Rhodobacteraceae serving as indicators of seawater intrusion. Community assembly analyses showed that homogeneous selection predominated, especially under strong salinity gradients, while dispersal limitation and spatial distance also contributed in areas of reduced connectivity. Key chemical factors, including TDS, Na⁺, Cl⁻, Mg²⁺, and K⁺, strongly shaped groundwater communities. Additionally, groundwater bacterial networks were more complex and robust than those in reservoir water, suggesting enhanced resilience to salinity stress. Collectively, this study demonstrates that salinity gradients can override the effects of hydraulic connectivity in structuring bacterial communities and their networks at coastal interfaces. Our findings provide novel microbial insights relevant for understanding biogeochemical processes and support the use of microbial indicators for more sensitive monitoring and management of coastal groundwater resources. Full article

Blue-green algae blooms present persistent environmental challenges in freshwater ecosystems, yet ecological interactions within the bacterial communities of Cylindrospermopsis-bloom reservoirs remain poorly understood. In this study, water samples were collected from February to May 2024 from 11 sampling sites in a Cylindrospermopsis-bloom reservoir in western Guangdong province, China. At each sampling point, a water sample was collected every month. High-throughput sequencing was applied to analyze the interaction between Cylindrospermopsis and other bacteria. As shown in our results, the phyla Actinobacteriota, Proteobacteria, Bacteroidota, Verrucomicrobiota, and Cyanobacteria were revealed as dominant phyla. Bacterial communities exhibited significant seasonal differences between flood and non-flood periods (ANOSIM: R = 0.472, p = 0.001). Cylindrospermopsis (dominance index Y = 0.53) acted as the keystone in the co-occurrence network (Z_i < 2.5, P_i > 0.62) and closely interacted with other bacteria. For better management of the blue-green algae bloom reservoir, the phyla of Actinobacteriota, Dependentiae, Acidobacteriota, Armatimonadota, Gemmatimonadota, and Desulfobacterota were proposed as microbial indicators for the eutrophic process. This study provides a new insight into the interactions of Cyanobacteria with other bacteria and the management of blue-green algae outbreaks in reservoirs. Full article

Integrated agriculture–aquaculture (IAA), represented by integrated rice–fish farming, offers a sustainable production method that addresses global food issues and ensures food security. Partitioned recirculating renovation based on traditional integrated rice–fish farming is an effective way to facilitate the convenient harvesting of aquatic products and avoid difficulties associated with mechanical operations. To elucidate the impact of partitioned recirculating renovation on the bacterial communities within paddy field ecosystems, we investigated the soil environmental conditions and soil bacterial communities within integrated rice–fish farming, comparing those with and without partitioned recirculating renovations. The findings indicated a significant reduction in the bacterial community richness within paddy soil in the ditch (fish farming area), along with noticeable changes in the relative proportions of the predominant bacterial phyla in both the ditch and the rice cultivation area following the implementation of partitioned recirculating renovation. In both the ditch and the rice cultivation area, partitioned recirculating renovation diminished the edges and nodes in the co-occurrence networks for soil bacterial communities and considerably lowered the robustness index, negatively impacting the stability of bacterial communities in paddy soil. Simultaneously, the partitioned recirculating renovation substantially influenced the bacterial community assembly process, enhancing the relative contributions of stochastic processes such as dispersal limitation, drift, and homogenizing dispersal. In addition, partitioned recirculating renovation significantly altered the soil environmental conditions in both the ditch and the rice cultivation area, with environmental factors being markedly correlated with the soil bacterial community, especially the total nitrogen (TN) and total phosphorus (TP), which emerged as the primary environmental drivers influencing the soil bacterial community. Overall, these results elucidated the ecological impacts of partitioned recirculating renovation on the paddy soil from a microbiomic perspective, providing a microbial basis for optimizing partitioned rice–fish systems. Full article

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

Biological nitrogen (N) fixation is an ecological method used to provide nutrition for crops and reduce fertilizer application in terrestrial ecosystems. Silver nanoparticles (AgNPs) are becoming environmental contaminants, and, thus, could negatively affect the activity and diversity of soil diazotrophs. To test this, a greenhouse pot experiment for growing maize was performed under different concentrations of AgNPs (0, 1, 5, 10, 20 mg kg⁻¹). We measured the N₂-fixation activity and abundance of nifH gene encoding the nitrogenase reductase subunit and analyzed the diversity, composition and co-occurrence networks of diazotrophic communities in maize rhizospheric soil. Results showed that a lower dose of AgNPs did not show significant influence on soil diazotrophs, while a higher dose of AgNPs decreased both soil N₂-fixation activity and nifH gene abundance, though diazotrophic diversity remained unchanged. AgNPs at 10 mg kg⁻¹ and 20 mg kg⁻¹ strongly shifted the community composition of diazotrophs, increasing the proportions of Bradyrhizobium and Paenibacillus, while decreasing Azospirillum and Rhizobium. Network analysis revealed weakened negative associations among species under AgNPs, with keystone taxa shifting from Bradyrhizobium, Geobacter, Azospirillum and Burkholderia to Bradyrhizobium, Paenibacillus and Skermanella under AgNPs. Soil-soluble Ag, dissolved organic carbon and soil pH were identified as the factors most closely driving the diazotrophic community composition. In conclusion, higher doses of AgNPs could inhibit N₂-fixation activity and shape the diazotrophic communities. These findings provide empirical evidence of AgNPs’ ecological impacts on soil microbial functions. Full article

Soil microorganisms play critical roles in mediating soil fertility. Exploring the effect of fertilization on soil microbial communities is of great importance to comprehend the sustainability of agriculture. However, the impacts of the application of different fertilization techniques on soil microbial communities remain ambiguous due to inconsistent findings across studies. In this study, we investigated changes in soil microbial communities under different fertilization techniques (chemical fertilizer (CK), organic fertilizer (OF), Bacillus-amended biofertilizer (BF), and Trichoderma-amended biofertilizer (MF)) and analyzed the link between soil fertility improvement and crop yield increase from a microbial perspective. Compared to the CK treatment, the BF and MF treatments increased corn yields by 16.07% and 12.98%, and soybean yields by 17.48% and 15.32%, respectively. BF tends to increase soil available phosphorus, whereas MF demonstrates a more pronounced enhancement in both available phosphorus and NH₄⁺-N contents. These differential effects were primarily linked to changes in the microbial community. Specifically, BF significantly enriched Bacillus, Rhodanobacter, Massilia, Mortierella, and Tetracladium, while the MF selectively increased the abundances of Burkholderia-Caballeronia-Paraburkholderia, Trichoderma, Penicillium, and Sistotrema. Co-occurrence network analysis revealed that biofertilizers enhanced microbial network stability and complexity compared to conventional fertilization techniques. Moreover, structural equation modeling (SEM) confirmed strong and positive relationships between crop yields and the abundances of specific probiotic microorganisms. These findings elucidate the mechanism-specific roles of biofertilizers in agricultural systems and provide novel insights for developing targeted biofertilizer formulations to advance sustainable agricultural practices. Full article

Soil microbial communities are essential for the natural attenuation of organic pollutants, yet their ecological responses under long-term contamination remain insufficiently understood. This study examined the bacterial community structure and the abundance of dechlorinating bacteria at a decommissioned pharmaceutical-chemical site in northern Jiangsu Province, China, where the primary pollutants were dichloromethane, 1,2-dichloroethane, and toluene. Eighteen soil samples from the surface (0.2 m) and deep (2.2 m) layers were collected using a Geoprobe-7822DT system and analyzed for physicochemical properties and microbial composition via 16S rRNA gene amplicon sequencing. The results showed that the bacterial community composition was significantly shaped by the soil pH, moisture content, pollutant type, and depth. Dechlorinating bacteria were detected at all sites but exhibited low relative abundance, with higher concentrations in the surface soils. Desulfuromonas, Desulfitobacterium, and Desulfovibrio were the dominant dechlorinators, while Dehalococcoides appeared only in the deep soils. A network analysis revealed positive correlations between the dechlorinators and BTEX-degrading and fermentative taxa, indicating potential cooperative interactions in pollutant degradation. However, the low abundance of dechlorinators suggests that the intrinsic bioremediation capacity is limited. These findings provide new insights into microbial ecology under complex organic pollution, and support the need for integrated remediation strategies that enhance microbial functional potential in legacy-contaminated soils. Full article

Engineering disturbances are increasing in permafrost regions of northeastern China, where soil microorganisms play essential roles in biogeochemical cycling and are highly sensitive to linear infrastructure disturbances. However, limited research has addressed how microbial communities respond to different post-engineering-disturbance recovery stages. This study investigated the impacts of the China–Russia Crude Oil Pipelines (CRCOPs) on soil microbial communities in a typical boreal forest permafrost zone of the Da Xing’anling Mountains. Soil samples were collected from undisturbed forest (the control, CK); short-term disturbed sites associated with Pipeline II, which was constructed in 2018 (SD); and long-term disturbed sites associated with Pipeline I, which was constructed in 2011 (LD). Pipeline engineering disturbances significantly increased soil clay content and pH while reducing soil water content (SWC), soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) (p < 0.05). No significant differences in these soil properties were observed between SD and LD. Bacterial diversity increased significantly, whereas fungal diversity significantly decreased following pipeline disturbances (p < 0.05). The beta diversity of both bacterial and fungal communities differed significantly among the three disturbance types. At the phylum level, pipeline disturbance increased the relative abundances of Proteobacteria, Acidobacteriota, Actinobacteriota, Ascomycota, and Mortierellomycota while reducing those of Bacteroidota and Basidiomycota. These shifts were associated with disturbance-induced changes in soil properties. Microbial co-occurrence networks in SD exhibited greater complexity and connectivity than those in CK and LD, suggesting intensified biotic interactions and active ecological reassembly during the early recovery phase. These findings suggest that pipeline disturbance could drive soil microbial systems into a new stable state that is difficult to restore over the long term, highlighting the profound impacts of linear infrastructure on microbial ecological functions in cold regions. This study provides a scientific basis for ecological restoration and biodiversity conservation in permafrost-affected areas. Full article