Search Results (14)

Urbanization-driven land use transitions, especially impervious surface expansion, profoundly affect aquatic ecosystems, yet the regulatory mechanisms of microbial assembly and disassembly remain unclear. Using environmental DNA metabarcoding, this study examined relationships between landscape patterns, environmental gradients, and microbial communities in the middle-lower Yangtze River. Impervious surfaces (source landscapes) increased from 10% (midstream) to 37% (downstream), disrupting source–sink balance, elevating nitrogen and phenolics, and worsening water quality. Eukaryotes exhibited higher α-diversity and more complex co-occurrence networks, showing greater responsiveness to disturbance. Stochastic processes dominated community assembly (>68%) for both eukaryotic and prokaryotic communities. Dispersal limitation led to higher total β-diversity and nestedness in eukaryotes; by contrast, land use intensified environmental filtering on prokaryotes, resulting in lower β-diversity but higher turnover contribution. Community disassembly simulation reveals a scenario in which impervious surface expansion is associated with non-random species loss, reducing predicted functional richness of both eukaryotic and prokaryotic microbes; the preferential loss of sensitive species is associated with a sharp decline in predicted functional richness, which may have implications for ecosystem stability. Our findings demonstrate that land use change is significantly associated with altered aquatic environments and affects ecosystem functions through biodiversity changes, providing theoretical support for ecosystem conservation. Full article

Background: Neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and amyotrophic lateral sclerosis (ALS), differ in etiology but share several convergent pathological mechanisms. Pterostilbene (PTR) is a natural stilbene with reported antioxidant, anti-inflammatory, and neuroprotective properties. This study aimed to prioritize putative PTR-associated targets and biological processes potentially relevant to shared neurodegenerative mechanisms. Methods: An integrative in silico workflow combining network pharmacology, protein–protein interaction (PPI) analysis, GO Biological Process (GO BP) enrichment, molecular docking, and molecular dynamics (MD) simulations was applied. GO BP terms were filtered, focused on neurodegeneration- and neuroprotection-related processes, and subjected to REVIGO-based redundancy reduction. Selected targets were further evaluated by docking and 500 ns MD simulations. Results: A total of 181, 165, 128, and 109 shared PTR–disease targets were identified for AD, PD, HD, and ALS, respectively. Redundancy-reduced GO BP analysis indicated associations with neuroinflammation, oxidative stress and reactive oxygen species-related responses, programmed cell death, MAPK/ERK- and PI3K/AKT-related signaling, ion and calcium transport, and lipid-, steroid-, or hormone-associated regulation. PPI topology prioritized SRC, ESR1, and HSP90AA1 as recurrent hub–bottleneck proteins, whereas MD-based structural interpretation focused on ESR1 and HSP90AA1. MD analyses indicated stable PTR interactions with both proteins, with ESR1 showing the most favorable predicted interaction profile. Conclusions: These findings suggest that PTR may interact with shared neurodegeneration-relevant molecular systems, particularly through ESR1- and HSP90AA1-associated mechanisms. However, the results are exclusively computational and should be interpreted as hypothesis-generating, requiring further experimental validation. Full article

Arid rangelands face increasing threats from grazing pressure and climate variability, yet the combined effects of grazing intensity and environmental gradients on plant community structure remain poorly understood. This study investigates grazing impacts on plant communities in southern Tunisia using floristic composition, ecological indicators, and indicator species across 500 plots representing low, moderate, and high grazing intensities. Vegetation surveys during peak growth recorded 386 vascular plant species. Species diversity peaked under moderate grazing (H’ = 5.46), consistent with the Intermediate Disturbance Hypothesis, but was strongly influenced by soil nitrogen (r² = 0.692). Heavy grazing reduced diversity (H’ = 4.82), especially in nitrogen-poor sites, indicating that environmental stress amplifies grazing effects. Indicator species analysis identified 113 significant taxa, including 42 associated with moderate grazing, reflecting compositional rather than functional responses. Redundancy analysis showed that environmental variables explained 67% of community variance, with soil nitrogen as the dominant gradient, followed by sand content, minimum temperature, and longitude. Ordination analyses revealed distinct assemblages under high grazing intensity associated with sandy, nutrient-poor soils. These findings demonstrate that grazing impacts are highly context-dependent and support the need for site-specific, soil-informed grazing management under increasing climate stress. Full article

Traditional prebiotic chemistry experiments often isolated single reactions under clean, controlled conditions, yet early Earth was chemically diverse and physically dynamic. Such primordial complexity likely imposed obstacles, including side reactions, low yields, and unstable intermediates, but it also generated opportunities, including redundant routes, parallel pathways, and environmental filters that could bias mixtures toward subsets of persistent and chemically productive compounds. This review examines how heterogeneous prebiotic settings could generate RNA precursors, including nucleobases, ribose, and phosphate-containing species, through multiple concurrent pathways. Although side reactions can sequester carbon in inert tars and reduce yields of specific targets, networked chemistry can also enhance robustness when different routes converge on shared intermediates, or when apparent byproducts reenter productive cycles. Environmental factors such as ultraviolet irradiation, mineral surfaces, wet-dry cycling, and thermal gradients can act as constraints that enrich certain products by differential stability, reactivity, and compartmentalization. In this context, the RNA world hypothesis remains compelling, as RNA can store heritable sequence information and catalyze reactions through sequence dependent folding, thereby linking heredity and chemistry within a single polymer. At the same time, the emergence of functional sequence information and of control architectures that couple sequence to reproducible function remains a central open problem, and it sets clear limits on what chemistry alone can explain. Rather than dismissing messy mixtures as irrelevant noise, it is more accurate to treat them as the native context in which concentration mechanisms, environmental cycling, and selective persistence could enable the accumulation and survival of RNA related molecules. Full article

Urban ecosystems are structurally and functionally distinct from their natural counterparts, with anthropogenic management potentially altering fundamental ecological processes such as seasonal community dynamics and impairing their sustainability. However, the mechanisms through which management filters plant diversity across seasons remain poorly understood. This study tested the hypothesis that management acts as an abiotic filter, dampening seasonal community variations and increasing biotic homogenization in urban green spaces. In this respect, through an intensive, multi-seasonal case study comparing two Mediterranean urban green spaces under contrasting management regimes, we analysed plant communities across 120 plots over four seasons. Results reveal a contingency cascade under management: while the species composition remains relatively stable (+26% variability, p < 0.001), the demographic success becomes more contingent (+41%, p < 0.001), and the ecological dominance becomes highly stochastic (+90%, p < 0.001). This hierarchy demonstrates that management primarily randomizes which species achieve dominance, in terms of biomass and cover, from a pool of disturbance-tolerant generalists. A 260% increase in alien and cosmopolitan species and persistent niche pre-emption dominance–diversity patterns also indicate biotic homogenization driven by management filters (mowing, trampling, irrigation, and fertilization) that favors species resistant to mechanical stresses and induces a breakdown of deterministic community assembly. These processes create spatially and temporally variable assemblages of functionally similar species, explaining both high structural variability and persistent functional redundancy. Conversely, seasonally structured, niche-based assemblies with clear dominance–diversity progressions are observed in the unmanaged area. Overall, findings demonstrate that an intensive management homogenizes urban plant communities by overriding natural seasonal filters and increasing stochasticity. The study provides a mechanistic basis for sustainable urban green space management, indicating that reduced intervention can help preserve the seasonal dynamics crucial for sustaining biodiversity and ecosystem functioning. Full article

The “cost of domestication” hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used Saccharomyces cerevisiae, the world’s oldest domesticated fungus, as a model to investigate the genomic characteristics of deleterious variants arising from fungal domestication. Employing a graph-based pan-genome approach, we identified 1,297,761 single nucleotide polymorphisms (SNPs), 278,147 insertion/deletion events (indels; <30 bp), and 19,967 non-redundant structural variants (SVs; ≥30 bp) across 687 S. cerevisiae isolates. Comparing these variants with synonymous SNPs (sSNPs) as neutral controls, we found that the majority of the derived nonsynonymous SNPs (nSNPs), indels, and SVs were deleterious. Heterozygosity was positively correlated with the impact of deleterious SNPs, suggesting a role of genetic diversity in mitigating their effects. The domesticated isolates exhibited a higher additive burden of deleterious SNPs (dSNPs) than the wild isolates, but a lower burden of indels and SVs. Moreover, the domesticated S. cerevisiae showed reduced rates of adaptive evolution relative to the wild S. cerevisiae. In summary, deleterious variants tend to be heterozygous, which may mitigate their harmful effects, but they also constrain breeding potential. Addressing deleterious alleles and minimizing the genetic load are crucial considerations for future S. cerevisiae breeding efforts. Full article

Afrotropical inland waters are highly diverse ecosystems; however, they remain poorly studied, especially for rotifers. Here, we contributed to the knowledge of the rotifer species richness in the largely understudied African countries of Angola and Ghana. We assessed the roles of habitat type and a suite of abiotic environmental factors in determining rotifer species richness of Ghana. A total of 37 sites (Ghana 32, Angola 5) in 19 water bodies from a variety of aquatic habitat types were sampled. In Ghana, we identified 118 taxa (105 species or subspecies level, 13 identified to genus). We identified 15 taxa (13 species) in the Angola samples. For Ghana, 100 of 118 (~85%) taxa were new records for the country, of which 13 species (~11%) were also new records for Africa. Nearly all the species (~93%) were new records for Angola. Species richness was positively correlated with conductivity and reservoir habitat type and negatively with pH. Redundancy analysis (RDA), conducted at the species level for the Ghana dataset, indicated suites of species associated with latitude, longitude, temperature, TDS, or pH. We also evaluated the effect of climate on species distribution in 27 African countries by conducting a review of all reports from Africa to determine factors associated with species richness. A Spearman’s correlation confirmed a significant positive correlation between the number of rotifer species and the number of climatic regions (R = 0.53, p < 0.001) for certain countries, based on species distributions in relation to Köppen–Geiger climate regions. This fact validates the environmental heterogeneity hypothesis for African rotifers. Lastly, we predicted that rotifer species richness in Ghana, as a country with a tropical climate, could approach ~190 taxa, while in climatically heterogeneous Angola we predict ~200 taxa. This study contributes to our knowledge of rotifer biogeography and species richness patterns in Africa. Full article

We assessed the distribution of alien fishes in the Karun River Basin, Iran. Fish were collected from 39 sites during the November–December 2018 low-flow period. In total, 39 fish species from nine orders and 14 families were documented. Among these, 10 species were alien to the basin (986 individuals; 15.7%). Four species were the most abundant alien species and primarily in impounded, downstream reaches. Redundancy analysis (RDA) was conducted to identify the extent of changes in alien fish assemblages with environmental parameters. RDA1 and RDA2 accounted for 36.24% and 25.33% of the variation of alien species, respectively. Altitude, depth, electrical conductivity, water temperature, turbidity, dissolved oxygen, and river width were the most significant parameters affecting alien species distributions. We present a dual-pathway cause-and-effect hypothesis proposing that alien fish species presence causes declines in the ecological status of native fish communities. We then explore how human-induced aquatic ecosystem degradation creates opportunities for alien species to invade new ecosystems, further impacting native fish communities. Our study contributes insight into the cause and effect of the presence of alien fish species in the Karun River Basin and emphasizes the urgency of conservation measures to protect this critically endangered watershed. Full article

Fire is a crucial disturbance factor for the structure and function of forest ecosystems, as it directly or indirectly affects plant growth, animal life and soil biogeochemical properties. Here, the effects of different fire severities and key driving environmental factors on soil microbial diversity and biomass were investigated in taiga forests that had undergone light, moderate or heavy fires, more recently or in the past, with unburned taiga forest included as a control (CK). The sample sites were located in the Greater Khingan mountains in the northeast of China. Critical soil parameters were determined, and bacterial and fungal content was inferred from determined phospholipid fatty acids (TPLFAs). The results showed that (1) all three fire severities significantly increased the concentrations of soil microbial carbon (MBC), moisture content (MC) and total nitrogen content (TN), but they significantly decreased soil available potassium (AK) content compared with the CK. (2) Recent light and moderate fires significantly decreased the Simpson and Shannon indices of soil microbial communities compared to CK; moderate fire did not change the Menhinick and Margalef indices. (3) Following moderate fire disturbance, there were no significant differences (p > 0.05) in relative abundance of total soil bacteria (Ba), Gram-positive bacteria (G⁺), Gram-negative bacteria (G⁻) and content of TPLFAs compared to the control, either as a result of more recent fires or earlier fires. (4) Redundancy analysis revealed that soil MC, TN, soil organic carbon (SOC), available P (AP) and alkaline N (AN) all strongly significantly affected the composition of the microbial communities, with a total explanation of 85.16% of the data. The species diversity and biomass of Ba, G⁺, G⁻ and TPLFAs were in accordance with the intermediate disturbance hypothesis. The change pattern of soil fungi was in accordance with their own characteristics of reproduction and growth, which was in line with k-selection and ecological countermeasures. Full article

Ensuring connectivity in the countryside and cities is a key element of nature protection, allowing genetic fluxes between populations in fragmented ecosystems. We tested the hypothesis that artificial green corridors are effective for birds in the city of Cochabamba (Bolivia). We compared the following aspects of natural corridors, with generally preserved vegetation, to those of artificial corridors, constituting parks and gardens in a matrix of streets densely planted with trees: species abundance and richness, functional diversity, and the traits of bird communities. We used canonical redundancy analysis to relate species abundance to the corridor type, noise, tree vegetation structure, richness, and functional diversity. We also tested the explanatory factors for relationships with bird species richness, functional diversity, and traits. We found that most species were shared between the corridor types; the corridor type, nevertheless, had significant effects, with bird species in the green corridors being more common and heavier and having a lower beak depth/mass. By contrast, noise-reflecting urbanization deeply affected all of the studied traits, indicating large shifts in species composition. In conclusion, green corridors seem reliable enough to maintain birds at a level almost comparable to that in linear corridors, but noise is a limiting factor for efficiency for both types. Full article

Nitrogen availability is one of the critical determinants of agricultural yield. Biological nitrogen fixation, such as legume–rhizobia symbiotic association, might function as a solution to fix nitrogen. Using phytosulfokine (PSK)-α sequences as a query, Yu et al., 2022 performed a comprehensive genome-wide search of legume species to identify PSK-δ, a divergent pentapeptide differing in single amino acid. Furthermore, PSK-δ exhibited nodule-specific expression with lower expression in the root, substantiating the nodule-specific temporal expression and suggesting its role in nodule development and nitrogen fixation. Additionally, in planta functional characterization in Medicago truncatula using overexpression and Tnt1-insertion mutant analysis indicated the role of PSK-δ in symbiotic nodulation. Interestingly, a similar phenotype of MtPSKδ mutant (mtpskδ) with that of wild-type control led to the hypothesis of its functional redundancy with PSK-α in nodule organogenesis. Further investigation regarding its position in the Nod-factor signaling pathway revealed the downstream function of PSK-δ in association with MtENOD11 in regulating nodule formation. Full article

Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types—VNI, VNII, VNIV and VNB—as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population. Full article

Gradient analysis was used to determine factors driving small-scale variation of cloud forest communities harboring Magnolia dealbata, a threatened species and bioculturally relevant tree for the Chinantecan, Mazatecan, Nahuan, and Zapotecan ethnicities in southern Mexico. Particularly, we aimed to: (a) determine factors explaining major community gradients at different heterogeneity scales along a small-scale elevational gradient, (b) test the Decreasing and the Continuum hypotheses along elevation, and (c) classify vegetation to assist in identifying conservation priorities. We used a stratified random sampling scheme for 21 woody stands along a small-scale (352 m) elevational transect. Four main data matrices were used (presence-absence, density, basal area, and guild data). Through Non-metric Multidimensional Scaling (NMS), Principal Coordinates Analysis (PCoA), and distance-based Redundancy Analysis (db-RDA), we found that major community variation was explained by soil pH, displaying an outstanding vegetation discontinuity, separating the species-rich relic Oreomunnea-Ticodendron-stands from stands with higher importance values for M. dealbata. The high species richness observed was explained by a combination of the windward effect of dry-seasonal maximum cloud condensation gain and habitat differentiation-specialization, a phenomenon that may also explain the mid-peak hypothesis and ensure the survival of relic species. Sampling-truncation and conservation status also played a role in this. Our results do not support the Decreasing and Continuum hypotheses along elevation. Full article

Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated. Full article