Search Results (669)

Fertilization is a critical measure for vegetation restoration and ecological reconstruction in degraded grasslands. However, little is known about the long-term effects of different combinations of nitrogen (N), phosphorus (P), potassium (K) on plant and microbial communities in degraded grasslands. This study conducted a four-year (2017–2020) N, P, K addition experiment in the Khorchin Grassland, a degraded typical grassland located in Zhalute Banner, Tongliao City, Inner Mongolia, to investigate the effects of fertilization treatment on plant functional groups and microbial communities after grazing exclusion. Our results showed that the addition of P, NP, and NPK compound fertilizers significantly increased aboveground biomass of the plant community, which is mainly related to the improvement of nutrient availability to promote the growth of specific plant functional groups, especially annual and biennial plants and perennial bunchgrasses. However, the addition of N, P, and NP fertilizers significantly reduced the species diversity of the plant community. At the same time, the addition of N, P, and NP fertilizers and the application of N and NP significantly reduced fungal species diversity but had no significant effect on soil bacteria. Our study provides new insights into the relationships between different types of fertilization and plant community productivity and biodiversity in degraded grasslands over four years of fertilization, which is critical for evaluating the effect of fertilization on the restoration of degraded grassland. Full article

This comprehensive study investigates the spatial distribution of metals in surface water, their accumulation in fish tissues, and their impact on the gut microbiome dynamics of fish in the Qi River, Huanggang City, Hubei Province. Three distinct sampling regions were established: the mining area (A), the transition area (B), and the distant area (C). Our results revealed that metal concentrations were highest in the mining area and decreased with increasing distance from it. The bioaccumulation of metals in fish tissues followed the order of gut > brain > muscle, with some concentrations exceeding food safety standards. Analysis of the gut microbiota showed that Firmicutes and Proteobacteria dominated in the mining area, while Fusobacteriota were more prevalent in the distant area. Heavy metal pollution significantly altered the composition and network structure of the gut microbiota, reducing microbial associations and increasing negative correlations. These findings highlight the profound impact of heavy metal pollution on both fish health and the stability of their gut microbiota, underscoring the urgent need for effective pollution control measures to mitigate ecological risks and protect aquatic biodiversity. Future research should focus on long-term monitoring and exploring potential remediation strategies to restore the health of affected ecosystems. Full article

Arbuscular mycorrhizal fungi (AMF) play a vital role in the restoration of tropical forests by enhancing soil fertility, facilitating plant establishment, and improving ecosystem resilience. This study presents a comprehensive bibliometric analysis of global scientific output on AMF in the context of ecological restoration, based on 3835 publications indexed in the Web of Science and Scopus databases from 2001 to 2024. An average annual growth rate of approximately 9.45% was observed, with contributions from 10,868 authors across 880 journals. The most prominent journals included Mycorrhiza (3.34%), New Phytologist (3.00%), and Applied Soil Ecology (2.79%). Thematically, dominant research areas encompassed soil–plant interactions, phytoremediation, biodiversity, and microbial ecology. Keyword co-occurrence analysis identified “arbuscular mycorrhizal fungi,” “diversity,” “soil,” and “plant growth” as core topics, while emerging topics such as rhizosphere interactions and responses to abiotic stress showed increasing prominence. Despite the expanding body of literature, key knowledge gaps remain, particularly concerning AMF–plant specificity, long-term restoration outcomes, and integration of microbial community dynamics. These findings offer critical insights into the development of AMF research and underscore its strategic importance in tropical forest restoration, providing a foundation for future studies and informing ecosystem management policies. Full article

True slime molds (Eumycetozoa) remain under-explored globally, particularly in water-logged forest habitats. Despite evidence suggesting a high biodiversity potential in the Knyszyn Forest of north-eastern Poland, no systematic effort had previously been undertaken there. In the present survey, plant substrates from eight swampy sub-compartments were incubated for over four months, resulting in the detection of fifteen slime mold species. Four of these taxa are newly reported for northern and north-eastern Poland, while several have been recorded only a handful of times in the global literature. These findings underscore how damp, nutrient-rich conditions foster Eumycetozoa and demonstrate the effectiveness of moist-chamber culturing in revealing rare or overlooked taxa. Current evidence shows that, although slime molds may occasionally colonize living plant or fungal tissues, their influence on crop productivity and tree vitality is negligible; they are therefore better regarded as biodiversity indicators than as pathogens or pests. By establishing a replicable framework for studying water-logged environments worldwide, this work highlights the ecological importance of swamp forests in sustaining microbial and slime mold diversity. Full article

Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance. Full article

Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of 18 plots were considered in this study, with six plots for each fragment type. Intact interior forest (F), internal forest path fragment (IF), and external forest path fragment (EF) soils were sampled at 0–15, 15–30, and 30–45 cm depths and profiled through phospholipid-derived fatty acid (PLFA) chemotyping and amino sugar proxies for living microbiome and microbial-derived necromass assessment, respectively. Carbon fractionation was performed through the chemical oxidation method. Diversity indices (Shannon–Wiener, Pielou evenness, Margalef richness, and Simpson dominance) were calculated based on the determined fatty acids derived from the phospholipid fraction. The microbial biomass ranged from 85.1 to 214.6 nmol g⁻¹ dry soil, with the surface layers of F exhibiting the highest values (p < 0.01). Shannon diversity declined systematically from F > IF > EF. The microbial necromass varied from 11.3 to 23.2 g⋅kg⁻¹. Fragmentation intensified the stratification of carbon pools, with organic carbon decreasing by approximately 14% from F to EF. Our results show that EFs possess a declining microbiome continuum that weakens their carbon sequestration capacity in urban forests. Full article

Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness—28% lower than expected for similar ecosystems—likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments. Full article

Landslides are a common geological hazard in mountainous areas, causing significant damage to ecosystems and production activities. Near-natural ecological restoration is considered an effective strategy for post-landslide recovery. To investigate the impact of near-natural restoration strategies on the recovery of plant communities and soil in landslide-affected areas, we selected landslide plots in Lantian County at 1, 6, and 11 years post-landslide as study sites, surveyed plots undergoing near-natural restoration and adjacent undisturbed control plots (CK), and collected and analyzed data on plant communities and soil properties. The results indicate that vegetation succession followed a path from “human intervention to natural competition”: species richness peaked at 1 year post-landslide (D_m = 4.2). By 11 years, dominant species prevailed, with tree species decreasing to 4.1 ± 0.3, while herbaceous diversity increased by 200% (from 4 to 12 species). Soil recovery showed significant temporal effects: total nitrogen (TN) and dehydrogenase activity (DHA) exhibited the greatest increases after 1 year post-landslide (132% and 232%, respectively), and by 11 years, the available nitrogen (AN) in restored plots recovered to 98% of the CK levels. Correlations between plant and soil characteristics strengthened over time: at 1 year, only 6–9 pairs showed significant correlations (p < 0.05), increasing to 21–23 pairs at 11 years. Near-natural restoration drives system recovery through the “selection of native species via competition and activation of microbial functional groups”. The 6–11-year period post-landslide is a critical window for structural optimization, and we recommend phased dynamic regulation to balance biodiversity and ecological functions. 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

Integrated rice–crayfish (Oryza sativa–Procambarus clarkii) co-culture (RC) systems have gained prominence due to their economic benefits and ecological sustainability; however, the interactions between soil properties and microbial communities in such systems remain poorly understood. This study evaluated the effects of the RC systems on soil physicochemical characteristics and microbial dynamics in paddy fields of southern Henan Province, China, over the 2023 growing season and subsequent fallow period. Using a randomized complete design, rice monoculture (RM, as the control) and RC treatments were compared across replicated plots. Soil and water samples were collected post-harvest and pre-transplanting to assess soil properties, extracellular enzyme activity, and microbial community structure. Results showed that RC significantly enhanced soil moisture by up to 30.2%, increased soil porosity by 9.6%, and nearly tripled soil organic carbon compared to RM. The RC system consistently elevated nitrogen (N), phosphorus (P), and potassium (K) throughout both the rice growth and fallow stages, indicating improved nutrient availability and retention. Elevated extracellular enzyme activities linked to carbon, N, and P cycling were observed under RC, with enzymatic stoichiometry revealing increased microbial nutrient limitation intensity and a shift toward P limitation. Microbial community composition was significantly altered under RC, showing increased biomass, a higher fungi-to-bacteria ratio, and greater relative abundance of Gram-positive bacteria, reflecting enhanced soil biodiversity and ecosystem resilience. Further analyses using the Mantel test and Random Forest identified extracellular enzyme activities, PLFAs, soil moisture, and bulk density as major factors shaping microbial communities. Redundancy analysis (RDA) confirmed that total potassium (TK), vector length (VL), soil pH, and total nitrogen (TN) were the strongest environmental predictors of microbial variation, jointly explaining 74.57% of the total variation. Our findings indicated that RC improves soil physicochemical conditions and microbial function, thereby supporting sustainable nutrient cycling and offering a promising, environmentally sound strategy for enhancing productivity and soil health in rice-based agro-ecosystems. Full article

Traditional type I sourdoughs are being rediscovered and increasingly used in artisanal and industrial bakeries due to the unique taste and texture, potential health benefits, and longer shelf life they confer on to baked products. These unique properties are attributed to the diverse microbial communities of sourdough, comprising both yeasts and bacteria. The traditional preservation method for type I sourdough (i.e., continuous backslopping) may lead, over time, to taxonomic and functional rearrangements of its microbial communities. Consequently, significant deviations in the characteristics of baked products can occur. In this context, this review aims to summarize the recent literature on the long-term preservation and maintenance strategies for type I sourdough and highlight the essential role that microbial biological resource centers (mBRCs) could play in the preservation and sharing of sourdough microbiomes. Specifically, the identification of appropriate preservation methods, implementation of well-defined access and benefit-sharing protocols, and development of microbiome-specific datasets, should be encouraged within the context of mBRCs. These infrastructures are expected to play a pivotal role in preserving the microbiota of fermented foods, serving as a crucial element for innovation and the safeguarding of traditional foods and culinary heritage. Full article

Projections indicate that the global urban population is anticipated to reach 67.2% by 2050, accompanied by a threefold increase in urban built-up areas worldwide. Urbanization has profoundly transformed Earth’s natural environment, notably characterized by the drastic reduction and fragmentation of wildlife habitats. These changes contribute to local species extinction, leading to biodiversity loss and profoundly impacting ecological processes and regional sustainable development. However, within urban settings, certain ‘generalist’ species demonstrate survival capabilities contingent upon phenotypic plasticity. The co-evolution of gut microbiota with their hosts emerges as a key driver of this phenotypic plasticity. The presence of diverse gut microbiota constitutes a crucial adaptive mechanism essential for enabling hosts to adjust to rapid environmental shifts. This review comprehensively explores amniote gut microbial changes in the context of urbanization, examining potential drivers of these changes (including diet and environmental pollutants) and their potential consequences for host health (such as physiology, metabolism, immune function, and susceptibility to infectious and non-infectious diseases). Ultimately, the implications of the gut microbiome are highlighted for elucidating key issues in ecology and evolution. This understanding is expected to enhance our comprehension of species adaptation in the Anthropocene. Full article

Climate change has intensified over recent decades, prompting shifts in forest management strategies, particularly in the Sudetes region of Poland, where native species like Norway spruce (Picea abies), European beech (Fagus sylvatica), and silver fir (Abies alba) have historically dominated. To address these changes, non-native species such as Douglas fir (Pseudotsuga menziesii) have been introduced as potential alternatives. This study, conducted in the Jugów and Świerki forest districts, compared the soil properties and water retention capacities of Douglas fir (Dg) and Norway spruce (Sw) stands (age classes from 8–127 years) in the Fresh Mountain Mixed Forest Site habitat. Field measurements included temperature, humidity, organic matter content, water capacity, and granulometric composition. Results indicate that, in comparison to Sw stands, Dg stands were consistently linked to soils that were naturally finer textured. The observed hydrological changes were mostly supported by these textural differences: In all investigated circumstances, Dg soils demonstrated greater water retention, displaying a water capacity that was around 5% higher. In addition to texture, Dg stands showed reduced soil water repellency and a substantially greater organic matter content (59.74% compared to 27.91% in Sw), which further enhanced soil structure and moisture retention. Conversely, with increasing climatic stress, Sw soils, with coarser textures and less organic matter, showed decreased water retention. The study highlights the importance of species selection in sustainable forest management, especially under climate change. Future research should explore long-term ecological impacts, including effects on microbial communities, nutrient cycling, and biodiversity, to optimize forest resilience and sustainability. Full article

Winemaking involves a microbial ecosystem where yeast diversity, shaped by terroir and winemaking conditions, determines wine characteristics. Understanding the microbial diversity of vineyards and spontaneous fermentation is crucial for explaining a winery’s typical wine profile. Studying and inoculating indigenous strains make it possible to produce high quality wines, reflecting the production environment. This study analyzes the yeast species involved in 16 spontaneous fermentations (8 in 2022 and 8 in 2023) from grapes of four distinct vineyards under two sets of winemaking conditions. A total of 1100 yeast colonies were identified by MALDI-TOF and DNA sequencing techniques. Saccharomyces (S.) cerevisiae and Hanseniaspora uvarum were the most prevalent species, alongside significant populations of non-Saccharomyces yeasts such as Lachancea thermotolerans and Metchnikowia pulcherrima, which were the most abundant ones. Minor yeast species, including Aureobasidium pullulans, Starmerella bacillaris, Kazachstania servazzi, and other Hanseniaspora spp., were also detected. The results demonstrated that yeast diversity in spontaneous fermentations varied according to vineyard origin and winemaking conditions. Differences between the two vintages studied indicated that annual climatic conditions significantly influenced yeast diversity, especially among non-Saccharomyces species. This substantial diversity represents a valuable source of indigenous yeasts for preserving the typicity of a winery’s wines under controlled conditions. Full article

The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas. Full article