Search Results (1,822)

The remediation of contaminated soils is essential for restoring land productivity and soil health. Pteris vittata L., an arsenic hyperaccumulator, has been widely used for phytoremediation, yet its ecological effects on soil systems remain insufficiently understood. In this field study, we evaluated the influence of Pteris vittata L. remediation on soil physico-chemical properties, microbial diversity, and molecular ecological networks. The results showed that long-term arsenic contamination significantly reduced soil total carbon, total nitrogen, and available phosphorus, simplified bacterial network structures, and markedly altered the keystone taxa that maintain microbial interactions. In contrast, soils under Pteris vittata L. remediation exhibited higher nutrient availability, greater bacterial diversity, and more complex microbial networks than contaminated soils, indicating partial recovery of ecosystem functions. These findings demonstrate that Pteris vittata L. remediation can mitigate arsenic-induced soil degradation and provide an important scientific basis for assessing the long-term impacts of arsenic contamination and the role of remediation measures in soil health evolution. Full article

Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article

The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g–h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass. Full article

Invasive species can alter community composition and ecosystem functioning. In the subtidal rocky shores of Arraial do Cabo Bay, southeastern Brazil, the invasive coral Tubastraea spp. has established populations, raising concerns about long-term impacts on native benthic communities. This study investigates temporal shifts in β-diversity across 44 fixed plots containing Tubastraea spp., monitored over 383 days. Underwater photographic surveys and multivariate analyses identified nine distinct benthic community types, each forming mosaic structures of sessile organisms. Temporal β-diversity analyses revealed that only the group characterized by Tubastraea, crustose calcareous algae and the zoantharian Palythoa caribaeorum showed significant differences between species gains and losses over time, suggesting temporal-scale dependency. Key contributors to community dissimilarity included P. caribaeorum, crustose calcareous algae, turf, the sponge genus Darwinella, and Tubastraea. This study highlights the importance of considering both spatial and temporal heterogeneity when assessing the ecological impact of marine invasive species. Our findings underscore the need for multi-scale monitoring to fully understand the dynamics of tropical subtidal ecosystems under biological invasion. While numerous studies report a correlation between Tubastraea abundance and shifts in ecological diversity, this relationship may be weak, as critical drivers such as the complexity of community organization are rarely accounted for. Full article

Phosphorus is a key macronutrient central to the processes of energy and information storage and exchange in the cell. Single-celled photosynthetic organisms, including microalgae, accumulate intracellular reserves of phosphorus (mostly in the form of polyphosphate) essential for the maintenance of cell homeostasis during fluctuations of external phosphorus availability. The polyphosphate reserves in microalgal cells are formed by polyphosphate polymerases—a ubiquitous enzyme family represented mainly by prokaryotic (PPK-type, typical of prokaryotes, e.g., cyanobacteria) and VTC-type polyphosphate polymerases harbored by eukaryotic microalgae, although certain species possess both PPK and VTC types of the enzyme. This enzyme is important for the environmental fitness of microalgae dwelling in diverse habitats, as well as for the efficiency of microalgae-based systems for the biocapture of phosphate from waste streams and for upcycling this valuable nutrient to agricultural ecosystems via biofertilizer from microalgal biomass. This review summarizes the recent progress in the field of structure, regulation, and functioning of VTC in microalgae. In conclusion, biotechnological implications and perspectives of VTC as a target of microalgal cell engineering and bioprocess design for improved phosphate bioremoval efficiency and culture robustness are considered. Full article

Microplastic (MPL) and nanoplastic (NPL) contamination in soils is widespread, impacting soil invertebrates, microbial communities, and soil–plant systems. Here, we compiled the information from 100 research articles from 2018 onwards to enhance and synthesize the status quo of MPLs’ and NPLs’ impacts on such groups. The effects of these pollutants depend on multiple factors, including polymer composition, size, shape, concentration, and aging processes. Research on soil invertebrates has focused on earthworms and some studies on nematodes and collembolans, but studies are still limited to other groups, such as mites, millipedes, and insect larvae. Beyond soil invertebrates, plastics are also altering microbial communities at the soil–plastic interface, fostering the development of specialized microbial assemblages and shifting microbial functions in ways that remain poorly understood. Research has largely centered on bacterial interactions with MPLs, leaving understudied fungi, protists, and other soil microorganisms. Furthermore, MPLs and NPLs also interact with terrestrial plants, and their harmful effects, such as adsorption, uptake, translocation, and pathogen vectors, raise public awareness. Given the complexity of these interactions, well-replicated experiments and community- and ecosystem-level studies employing objective-driven technologies can provide insights into how MPLs and NPLs influence microbial and faunal diversity, functional traits, and soil ecosystem stability. Full article

Secondary metabolites, including alkaloids, flavonoids, and tannins, are crucial for human health, agriculture, and ecosystem functioning. Their synthesis is often species-specific, influenced by both genetic and environmental factors. The increasing demand for these compounds across various industries highlights the need for advancements in plant breeding and biotechnological approaches. Transcription activator-like effector nucleases (TALENs) have emerged as a powerful tool for precise genome editing, offering significant potential for enhancing the synthesis of secondary metabolites in plants. However, while plant genome editing technologies have advanced significantly, the application of TALENs in improving secondary metabolite production and expanding genetic diversity remains underexplored. Therefore, this review aims to provide a comprehensive analysis of TALEN-mediated genome editing in plants, focusing on their role in enhancing secondary metabolite biosynthetic pathways and improving genetic diversity. The mechanisms underlying TALENs are examined, including their ability to target specific genes involved in the synthesis of bioactive compounds, highlighting comparisons with other genome editing tools such as CRISPR/Cas9. This review further highlights key applications in medicinal plants, particularly the modification of pathways responsible for alkaloids, flavonoids, terpenoids, and phenolic compounds. Furthermore, the role of TALENs in inducing genetic variation, improving stress tolerance, and facilitating hybridization in plant breeding programs is highlighted. Recent advances, challenges, and limitations associated with using TALENs for enhancing secondary metabolite production are critically evaluated. In this review, gaps in current research are identified, particularly regarding the integration of TALENs with multi-omics technologies and synthetic biology approaches. The findings suggest that while underutilized, TALENs offer sustainable strategies for producing high-value secondary metabolites in medicinal plants. Future research should focus on optimizing TALEN systems for commercial applications and integrating them with advanced biotechnological platforms to enhance the yield and resilience of medicinal plants. Full article

Caves and other subterranean ecosystems are characterized by stable, low temperatures, high humidity, and limited nutrient input, creating unique environments for extremophilic microorganisms. Among them, fungi play key roles in organic matter degradation, mineral interactions, and biogeochemical cycling, yet the diversity and adaptations of cold-adapted fungi in cave habitats remain insufficiently explored. This study investigated psychrophilic and psychrotolerant fungi inhabiting the stone surfaces of Ravništarka Cave in Eastern Serbia. Biofilm samples were collected from nine sites and analyzed using culture-based isolation on both nutrient-rich and diluted media, followed by incubation at 10 °C, 25 °C, and 37 °C. Fungal identification combined morphological characteristics with molecular analyses of the ITS region and BenA gene, while ecological roles were assigned using FUNGuild. A total of 41 fungal species were documented, spanning Ascomycota (53.1%), Basidiomycota (43.7%), and Mortierellomycota (3.1%) phyla. The genus Penicillium exhibited the greatest species richness, with 14 taxa documented, including P. chrysogenum, P. glandicola, and P. solitum, all previously associated with cold or oligotrophic environments. The psychrotolerant species Mortierella alpina was the only representative of Mortierellomycota. Ecological guild assignment revealed fungi functioning at different trophic levels, highlighting their multifunctional ecological roles in extreme subterranean habitats. Full article

Background: The human gut microbiome—a diverse ecosystem of trillions of microorganisms—plays an essential role in metabolic, immune, and neurological regulation. However, modern lifestyle factors such as antibiotic overuse, cesarean delivery, reduced breastfeeding, processed and high-sodium diets, alcohol intake, smoking, and exposure to environmental toxins (e.g., glyphosate) significantly reduce microbial diversity. Loss of keystone species like Bifidobacterium infantis (B. infantis) and Lactobacillus reuteri (L. reuteri) contributes to gut dysbiosis, which has been implicated in chronic metabolic, autoimmune, cardiovascular, and neurodegenerative conditions. Materials and Methods: This Qualitative Systematic Review (QualSR) synthesized data from over 547 studies involving human participants and standardized microbiome analysis techniques, including 16S rRNA sequencing and metagenomics. Studies were reviewed for microbial composition, immune and metabolic biomarkers, and clinical outcomes related to microbiome restoration strategies. Results: Multiple cohort studies have consistently reported a 40–60% reduction in microbial diversity among Western populations compared to traditional societies, particularly affecting short-chain fatty acid (SCFA)-producing bacteria. Supplementation with B. infantis is associated with a significant reduction in systemic inflammation—including a 50% decrease in C-reactive protein (CRP) and reduced tumor necrosis factor-alpha (TNF-α) levels—alongside increases in regulatory T cells and anti-inflammatory cytokines interleukin-10 (IL-10) and transforming growth factor-beta 1 (TGF-β1). L. reuteri demonstrates immunomodulatory and neurobehavioral benefits in preclinical models, while both probiotics enhance epithelial barrier integrity in a strain- and context-specific manner. In murine colitis, B. infantis increases ZO-1 expression by ~35%, and L. reuteri improves occludin and claudin-1 localization, suggesting that keystone restoration strengthens barrier function through tight-junction modulation. Conclusions: Together, these findings support keystone species restoration with B. infantis and L. reuteri as a promising adjunctive strategy to reduce systemic inflammation, reinforce gut barrier integrity, and modulate gut–brain axis (GBA) signaling, indicating translational potential in metabolic and neuroimmune disorders. Future research should emphasize personalized microbiome profiling, long-term outcomes, and transgenerational effects of early-life microbial disruption. Full article

With the widespread adoption of large language models (LLMs) in code generation tasks, geospatial code generation has emerged as a critical frontier in the integration of artificial intelligence and geoscientific analysis. This growing trend underscores the urgent need for systematic evaluation methodologies to assess the generation capabilities of LLMs in geospatial contexts. In particular, geospatial computation and visualization tasks in the JavaScript environment rely heavily on the orchestration of diverse frontend libraries and ecosystems, posing elevated demands on a model’s semantic comprehension and code synthesis capabilities. To address this challenge, we propose GeoJSEval—the first multimodal, function-level automatic evaluation framework for LLMs in JavaScript-based geospatial code generation tasks. The framework comprises three core components: a standardized test suite (GeoJSEval-Bench), a code submission engine, and an evaluation module. It includes 432 function-level tasks and 2071 structured test cases, spanning five widely used JavaScript geospatial libraries that support spatial analysis and visualization functions, as well as 25 mainstream geospatial data types. GeoJSEval enables multidimensional quantitative evaluation across metrics such as accuracy, output stability, resource consumption, execution efficiency, and error type distribution. Moreover, it integrates boundary testing mechanisms to enhance robustness and evaluation coverage. We conduct a comprehensive assessment of 20 state-of-the-art LLMs using GeoJSEval, uncovering significant performance disparities and bottlenecks in spatial semantic understanding, code reliability, and function invocation accuracy. GeoJSEval offers a foundational methodology, evaluation resource, and practical toolkit for the standardized assessment and optimization of geospatial code generation models, with strong extensibility and promising applicability in real-world scenarios. This manuscript represents the peer-reviewed version of our earlier preprint previously made available on arXiv. Full article

Rapid urbanization has resulted in widespread habitat loss and fragmentation, threatening global biodiversity. Urban parks serve as essential refuges for wildlife within cities, particularly for birds, which are sensitive indicators of ecosystem health and habitat quality. In recent years, numerous Chinese cities have begun integrating biodiversity-friendly design approaches into new park development. However, the effectiveness of these strategies remains insufficiently evaluated. This study assesses the ecological performance of newly built parks by examining 11 recently constructed parks (within the past decade) and 9 historical parks in Zhengzhou, China’s high-density urban area. Monthly bird surveys were conducted across all 20 parks from May to December 2020, covering breeding, post-breeding, and overwintering seasons. Our findings reveal that new parks significantly outperformed old parks in bird abundance, species richness, Shannon diversity index, and functional diversity. Analysis of environmental variables at both local (within-park) and landscape (1-km buffer) scales showed that habitat diversity and multi-layered vegetation structure were the most influential local factors promoting bird diversity, while green space connectivity was the primary landscape-scale contributor. Notably, neither park area nor age significantly predicted diversity patterns. Based on these results, we propose three key planning strategies: (1) enhancing habitat diversity within parks to support species from various ecological niches; (2) implementing multi-layered vegetation planting to provide diverse food resources and nesting opportunities; (3) improving green space connectivity to facilitate species movement and population persistence within urban environments. These findings provide valuable insights for designing more effective biodiversity-friendly urban green spaces. Full article

In tropical regions, the establishment of large-scale exotic plantations has addressed the demand for timber resources but has also disrupted the structural stability of native vegetation and altered soil nutrient cycling, thereby impairing ecosystem functions. Identifying effective restoration strategies for these plantations is crucial for sustainable forest management and ecological security. This study examined Acacia mangium Willd., Cunninghamia lanceolata (Lamb.) Hook., and Pinus caribaea Morelet. plantations in Hainan Tropical Rainforest National Park under three treatments: plantation control, girdling, and natural secondary forest. Vegetation surveys and soil analyses were conducted to explore the relationships between community structure, soil physicochemical properties, and enzyme activities. Diversity indices, Pearson correlations, and redundancy analysis were used to assess plant–soil relationships. The results showed that girdling significantly accelerated succession in C. lanceolata and P. caribaea plantations, increased species diversity, and enhanced the dominance of native species. Shrub-layer diversity indices (H_shrub, D_shrub, E_shrub) were the main drivers of soil properties and enzyme activities, while tree-layer effects were weaker. Girdling regulated soil nutrients and biological activity primarily via changes in community structure. These findings highlight the importance of optimizing shrub-layer structure and enhancing diversity for tropical plantation restoration. Combining forest type conversion with moderate interventions can promote coordinated plant–soil development over time. Full article

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline–alkali soils and plant organs remains poorly characterized. In this study, the V3–V4 variable region of the endophytic bacteria 16S rRNA gene in three organs (roots, leaves, and pods) of high-oleic-acid peanut variety Huayu9118 from three saline–alkali locations (Xinjiang, Jilin, and Shandong, China) was analyzed by high-throughput sequencing. A total of 1,360,313 effective sequences yielded 19,449 amplicon sequence variants (ASVs), with Proteobacteria (45.86–84.62%), Bacteroidota (6.52–13.90%), and Actinobacteriota (3.97–10.87%) dominating all samples. Niche strongly influenced microbial diversity: the roots exhibited the highest level of richness (Chao 1/ACE indices), while the leaves showed the greatest diversity (Shannon/Simpson indices) in XJ samples. Significant compositional differences were observed between aerial (leaves) and underground (roots/pods) organs. Geographic location also markedly shaped endophytic communities, with stronger effects in roots and pods than in leaves—a pattern supported by PCoA combined with ANOSIM (R (roots) = 1, R (pods) = 0.874, R (leaves) = 0.336, respectively, p < 0.001). Saline–alkali adaptation led to a marked enrichment of Novosphingobium in roots and pods and of Halomonas in leaves compared to non-saline–alkali-grown peanuts. Furthermore, the endophytic communities within the same organ type varied significantly across the three saline–alkali sites. Redundancy analysis (RDA) identified the key environmental factors shaping bacterial community composition in the root samples from each location: available phosphorus (AP) and sulfate (SO₄²⁻) were the strongest predictors in XJ; available potassium (AK) and chloride (Cl⁻) in DY; and hydrolyzed nitrogen (HN), pH, soil organic matter (SOM), and bicarbonate (HCO₃⁻) in JL. These findings demonstrate that niches and geographical conditions determined the composition and relative abundance of endophytic bacteria in salt-tolerant peanuts, providing new insights into microbial ecological adaptation in saline–alkali ecosystems. Full article

The human gut microbiota constitutes the microbial ecosystem within the human gut. It consists of trillions of mostly prokaryotic microorganisms living in the gut lumen, which have an active metabolic role in the regulation of many host functions, including vitamin synthesis and energy extraction from indigestible fiber. Host diet is the main driver of gut microbial composition and metabolic output. Athletes and athletic individuals often supplement their diet with legal nutritional supplements to enhance performance, especially at the elite level. This review summarizes and critically comments on key evidence of the effects of the most common athletic nutritional supplements on the human gut microbiota, based on the most recent literature. We cover suggested changes in bacterial diversity or the relative abundance of specific bacterial taxa and effects of nutritional supplementation on bacterial metabolism. We focus on the molecular pathways involved, we discuss contrasting results and inconsistencies, and we note limitations and challenges in the field. We conclude with a summary of evidence, proposals, and future directions. Full article

The health of ecosystems, their functionality and the fulfilment of ecosystem functions are all dependent on biodiversity and productivity. The ongoing transformation of forests is intensifying the need for conservation. At the same time, the herbaceous layer has not yet been studied enough by researchers. The aim of the study is to ascertain the impact of the composition and age of the stand of primary and secondary forests on the biomass and species diversity of the herbaceous layer in the most prevalent forest type of the Western Macroscline of the Southern Urals: moss spruce forests. The methodological basis was chosen to be genetic forest typology and generally accepted methods of studying forest vegetation. We studied primary dark coniferous forests, as well as secondary birch and aspen forests of different compositions and ages. Positive correlations with the age of the stand were found to be most pronounced for Oxalis acetosella L. and Lycopodium clavatum L., while negative correlations were found to be most pronounced for Deschampsia caespitosa (L.) P. Beauv., Brachypodium pinnatum (L.) Beauv., and Dactylis glomerata L. The positive correlations with the proportion of birch and aspen in the stand composition are most pronounced for Dactylis glomerata L., Geum rivale L., Aegopodium podagraria L., Aconitum septentrionale Koelle, and Prunella vulgaris L. The research results clearly demonstrate the length of time that changes in species composition and productivity of the herbaceous layer of mountain forests take place over. This must be considered when planning forest management and nature conservation in mountain forests in the Urals. On the one hand, our study is certainly regional, but on the other, similar forests, forest degradation, regenerative succession and the plant species studied are widespread in the boreal zone. Therefore, the research results will be of interest to many researchers whose work relates to forest resources, biodiversity conservation and forest succession. To expand the scope of the research, further studies are planned in other types of forest in the Ural Mountains. Full article