Search Results (487)

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

AM fungi play a pivotal role in regulating ecosystem functioning and processes. However, the assembly of soil AM fungal communities and its drivers across Populus euphratica forests in extremely arid regions remain largely unclear. Here, we explored the composition and assembly processes of AM fungal communities in the soil of P. euphratica forests in northwest China. The results showed that soil salinity affected the composition, assembly processes, and network stability and complexity of AM fungal communities. Stochastic processes rather than deterministic processes dominated the community assembly of AM fungi. Habitat generalists were more susceptible to deterministic processes than specialists. In addition, the network analysis showed that fungal network complexity had a hump-shaped relationship with increasing soil salinity, while network stability had a U-shaped relationship. This research suggests that soil salinity plays an essential role in determining AM fungal community composition and assembly processes in P. euphratica forests of arid regions. Full article

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems. 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

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

Citrus is one of the most widely consumed fruits in the world, and its cultivation industry continues to develop rapidly. However, the roles of soil protistan communities during citrus growth are not yet fully understood, despite the potential significance of these communities to the health and quality of citrus. In this study, we examined the soil properties and protistan communities in Eureka lemon farmlands located in Chongqing, China, during the flowering and fruiting stages of cultivation, both in greenhouse and open-field settings. In general, the majority of the measured soil properties (including nutrients and enzyme activities) exhibited higher values in open-field farmlands in comparison to those observed in greenhouse counterparts. According to the results of high-throughput sequencing based on the V9 region of eukaryotic 18S rRNA gene, the diversity of soil protistan communities was also higher in open-field farmlands, and both lemon growth stage and cultivation modes showed significant effects on soil protistan compositions. The transition from traditional agricultural practices to greenhouse farming resulted in a significant transformation of the soil protistan community. This transformation manifested as a shift towards a state characterized by diminished nutrient cycling capabilities. This decline was evidenced by an increase in phototrophs (Archaeplastida) and a concomitant decrease in consumers (Stramenopiles and Alveolata). Community assembly analysis revealed deterministic processes that controlled the succession of soil protistan communities in lemon farmlands. It has been established that environmental associations have the capacity to recognize nitrogen in soils, thereby providing a deterministic selection process for protistan community assembly. Furthermore, a production index was calculated based on 12 quality parameters of lemons, and the results indicated that lemons from greenhouse farms exhibited a lower quality compared to those from open fields. The structure equation model revealed a direct correlation between the quality of lemons and the cultivation methods employed, as well as the composition of soil protists. The present study offers insights into the mechanisms underlying the correlations between the soil protistan community and lemon quality in response to changes in the cultivation modes. 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

This study examines how climate citizens’ assemblies (CCAs) influence youth engagement, both in practice and in shaping perceptions of political “voice”, drawing on Albert O. Hirschman’s “Exit, Voice, and Loyalty” framework. Through qualitative analysis of 71 interviews, participatory workshops, and observational data across four cities—Barcelona, Bologna, Geneva, and Paris—it explores whether CCAs address youth climate activists’ demands, enable meaningful participation, and yield policy outcomes aligned with their claims. Findings reveal divergent perceptions: in Bologna, co-design with activists tended to foster trust, while Barcelona saw disillusionment due to unmet expectations. Geneva’s embedded deliberative processes strengthened institutional loyalty, whereas Paris faced skepticism as activists turned to civil disobedience. Overall, CCAs’ effectiveness hinges on inclusivity, follow-through, and communication; when perceived as tokenistic, they risk reinforcing disengagement (“exit”). The study underscores the need for embedded, responsive democratic innovations to sustain youth participation amid climate crises. Full article

The Qinghai–Tibet Plateau is a key region for biodiversity conservation, where alpine grasslands are ecologically important. While previous studies have mainly addressed vegetation, ecosystem processes, and soil microbes, phyllosphere microorganisms are essential for nutrient cycling, plant health, and stress tolerance. However, their communities remain poorly understood compared to those in soil. The relative influence of host identity and environmental conditions on shaping phyllosphere microbial diversity and community assembly remains uncertain. In this study, we characterized phyllosphere bacterial and fungal communities of the phyllosphere at two alpine steppe sites with similar vegetation but climatic conditions: the Qilian Mountains (QLM) and the Qinghai Lake region (LQS). At both sites, Cyanobacteriota and Ascomycota were the predominant bacterial and fungal taxa, respectively. Microbial α-diversity did not differ significantly between the two regions, implying that host-associated mechanisms may stabilize within-site diversity. In contrast, β-diversity exhibited clear spatial differentiation. In QLM, bacterial β-diversity was significantly correlated with mean annual precipitation, while fungal α- and β-diversity were associated with soil nutrient levels (including nitrate, ammonium, available potassium, and phosphorus) and vegetation coverage. At LQS, the β-diversity of both bacterial and fungal communities was strongly influenced by soil electrical conductivity, and fungal communities were further shaped by vegetation cover. Community assembly processes were predominantly stochastic at both sites, although deterministic patterns were more pronounced in QLM. Variability in moisture availability contributed to random bacterial assembly at LQS, while increased environmental heterogeneity promoted deterministic assembly in fungal communities. The elevated diversity of microbes and plants in QLM also reinforced deterministic processes. Overall, our findings support a host–environment interaction hypothesis, indicating that host factors primarily govern α-diversity, while climatic and soil-related variables have stronger effects on β-diversity and microbial assembly dynamics. These insights advance our understanding of how phyllosphere microbial communities may respond to environmental change in alpine ecosystems. Full article

Urban green spaces are integral components of city ecosystems, supporting essential belowground microbial communities such as arbuscular mycorrhizal fungi (AMF). Understanding how green space types influence AMF communities is key to promoting urban ecological function. This study examines AMF diversity, community assembly, and co-occurrence network structures in two urban green space types—park and roadside—in Kaifeng, Henan Province, China. Soil samples were collected from both sites, and AMF community composition was assessed using high-throughput sequencing. Environmental variables, including total nitrogen (TN), available phosphorus (AP), available potassium (AK), water content, and pH, were measured to evaluate their influence on AMF communities. The results indicate marked differences between the two green space types. Park soils support significantly greater AMF species richness and more complex co-occurrence networks than roadside soils. These differences are correlated with higher nutrient levels in park soils. By contrast, AMF communities in roadside soils are more strongly associated with soil water content and pH, resulting in reduced diversity and more homogeneous community structures. Stochastic processes predominantly govern community assembly in both green space types, with roadside green spaces being more influenced by stochastic processes than park green spaces. These findings highlight the influence of urban landscape type on AMF communities and provide guidance for enhancing urban biodiversity through targeted landscape planning and soil management. In future work, we will implement long-term AMF monitoring across different green-space types and evaluate specific management practices to optimize soil health and ecosystem resilience. Full article

Here, the biogeographic patterns of abundant and rare bacterial taxa in lemon farmlands with different cultivation modes were examined using the dataset obtained from high-throughput sequencing. The abundant sub-communities exhibited a lower richness, a similar abundance proportion, and lower compositional variations than rare taxa. With regard to different cultivation modes, a lower richness but higher beta-diversity distance was observed in abundant bacterial taxa from greenhouse soils compared to other open field farmlands. In addition, some potential indicators, including Proteobacteria, Chloroflexi, and Bacteroidota, were found to be enriched in the abundant sub-communities in greenhouse soils. Moreover, a stronger environmental-related distance–decay of similarity was observed in abundant taxa from greenhouse soils, but in hilly-converted farmlands for rare taxa. The abundant sub-communities were more sensitive to environmental changes and more tightly phylogenetically clustered. In contrast, homogeneous selection dominated the assembly of rare taxa, which was insensitive to dispersal limitations. Soil pH was identified as the key factor to driving the assembly of soil bacterial communities, with a more deterministic and stochastic assembly for abundant and rare taxa, respectively, at the neutral environments. Full article

The bacterial microbial community composition during wine fermentation is a key contributor to wine quality and flavor. However, studies on the regulatory effects of different grape varieties and co-fermentation processes on the microbial community structure and their synergistic mechanisms remain limited. In this study, Cabernet Sauvignon (CS) was subjected to single-variety fermentation and used as the base wine for co-fermentation with three other grape varieties—Marselan (CSMN), Merlot (CSMT), and Cabernet Gernischt (CSCG)—to systematically compare the differences in the microbial community composition and their effects on the production of metabolic compounds. The results showed that, compared with single-variety fermentation, co-fermentation significantly increased the α-diversity of microbial communities (the Shannon index increased) and exhibited significant differences in β-diversity (PERMANOVA analysis, R² = 0.421, p < 0.001). A neutral model analysis indicated that co-fermentation had a significant impact on microbial community assembly mechanisms, with the contribution of neutral processes to community assembly increasing from 45.5% (in the CSCG process) to 62.3% (in the CSMT process). A microbial co-occurrence network analysis revealed that co-fermentation enhanced the network complexity of microbial communities and strengthened the synergistic interactions between microbial taxa. A metabolic compound analysis revealed that co-fermentation significantly enhanced the production of key aroma compounds, resulting in increased concentrations of isoamyl acetate, ethyl hexanoate, linalool, and geraniol. These findings highlight the differences in microbial communities and their synergistic mechanisms among co-fermented grape varieties, providing theoretical guidance and practical insights for optimizing co-fermentation processes and improving wine quality. Full article

Systemic cancer progression culminating in metastatic disease is implicitly dependent on tumour cell interactions with the vascular system. Indeed, different facets of the micro- and macro-vasculature can be regarded as rate-limiting ‘vascular checkpoints’ in the process of cancer dissemination. The underlying complex communication networks drive tumour neovascularization, angiogenesis, immunoregulation, activation of the coagulation system, angiocrine interactions, and non-angiogenic vascular responses across multiple cancer types. Yet, each cancer may represent a unique vascular interaction scenario raising a prospect of targeted modulation of blood and lymphatic vessels for therapeutic purposes, beyond the traditional notion of tumour anti-angiogenesis. While the emphasis of studies aiming to understand this circuitry has traditionally been on soluble, or ‘mono-molecular’ mediators, the rise of the particulate secretome encompassing heterogeneous subpopulations of extracellular vesicles (EVs; including exosomes) and particles (EPs) brings another dimension into the tumour–vascular communication web during the process of metastasis. EVs and EPs are nanosized cellular fragments, the unique nature of which lies in their ability to encapsulate, protect and deliver to target cells a range of bioactive molecular entities (proteins, RNA, DNA) assembled in ways that enable them to exert a wide spectrum of biological activities. EVs and EPs penetrate through biological barriers and are capable of intracellular uptake. Their emerging vascular functions in metastatic or infiltrative cancers are exemplified by their roles in pre-metastatic niche formation, thrombosis, vasectasia or angiocrine regulation of cancer stem cells. Here, we survey some of the related evidence supporting the biological, diagnostic and interventional significance of EVs/EPs (EVPs) in disseminated neoplastic disease. Full article

This study examines the impact of continuous cropping (short-term: 1–8 years; medium-term: 9–15 years; long-term: 16–30 years) on soil microbial community diversity, co-occurrence networks, and assembly processes in Xinjiang’s cotton region, a globally recognized arid zone. The results are as follows. Soil physicochemical analyses showed that as continuous cropping duration increased, soil organic matter and total nitrogen significantly decreased, whereas available phosphorus and potassium increased, and the soil’s aggregate structure degraded. Microbial community analysis indicated that long-term continuous cropping notably increased the richness of bacterial species (Chao1 index) and altered fungal communities’ diversity and composition, especially increasing the relative abundance of Cladosporium and Alternaria in the long term (GY30). Co-occurrence network analysis revealed higher complexity in bacterial and fungal networks in the short term. As cropping duration increased, bacterial network complexity significantly decreased, while fungal networks partially recovered in the long term, indicating greater fungal adaptability to environmental changes. Assembly process analysis revealed that the assembly of bacterial and fungal communities was jointly regulated by stochastic and deterministic processes, but with increasing cropping duration, deterministic processes weakened while stochastic processes intensified. Soil available phosphorus, potassium, and pH were identified as key factors influencing microbial community succession and assembly. This study highlights the significance of co-occurrence networks and assembly processes for understanding the dynamics of continuous cropping’s impact on soil microbial communities, offering a theoretical foundation for improving agricultural management. Full article

The cold temperate forest ecosystem is a crucial ecological zone in China, significantly impacted by human activities. To understand the impact of restoration on soil microbial communities following disturbance, this study employed high-throughput sequencing technology to systematically examine the assembly patterns and processes of soil microbial communities under two restoration modes (nature restoration (NR) and artificial restoration (AR)) in this forest ecosystem. The results indicated that the concentrations of total nitrogen (TN), alkaline hydrolysable nitrogen (AN), dissolved organic carbon (DOC) and soil organic carbon (SOC) were significantly higher in soils under natural restoration compared to artificial restoration. The α-diversity of soil bacteria remained unchanged, while soil fungal α-diversity changed significantly across different restoration modes. Furthermore, different restoration modes significantly alter the β-diversity of soil microbial (bacterial and fungal) communities. The relative abundance of soil microbial (bacterial and fungal) changed significantly across different forest restoration strategies, i.e., the relative abundance of Pajaroellobacter increased in natural restoration compared to that in natural forest; similarly, both Podila and Russula showed higher relative abundances in natural restoration than those in natural forest. Furthermore, analysis of variance for differences between groups shows that Incoybe plays a crucial role in artificial restoration. Community assembly analyses indicated that that soil microbial (bacterial and fungal) communities were primarily driven by deterministic processes in both restoration models. In short, our study improves our comprehension of how soil microbial communities respond to different restoration methods in temperate forest ecosystems, providing valuable insights for their sustainable management. Full article