Search Results (426)

Skin is a highly specialized barrier organ, which serves essential barrier, immune, and sensory functions and exhibits conserved structure. In addition, each species exhibits a unique skin transcriptional profile for adapting distinct environmental conditions and physiological demands. However, these transcriptional profiles across mammals remain incompletely understood. In this study, we integrated 61 publicly available skin RNA-seq datasets from eight mammalian species: human (Homo sapiens), macaque (Macaca fascicularis), mouse (Mus musculus), sheep (Ovis aries), goat (Capra hircus), donkey (Equus asinus), rabbit (Oryctolagus cuniculus), and pig (Sus scrofa). We identified a large number (2286 to 4588) of differentially expressed genes (DEGs) based on 10,504 one-to-one orthologous genes in all pairwise species comparisons. A total of 44 conserved genes were identified by integrating tissue specificity, expression variability, and mean expression level, which were enriched in epidermal development, keratinocyte differentiation, and desmosome organization. We also identified species-specific genes and transcription factors, such as STMN1 (donkey), COL1A1 (goat), and ACTN2 (mouse), which are associated with the cell cycle, extracellular matrix, and muscle contraction pathways, respectively. WGCNA further revealed goat-associated module 2 (M2) enriched in the negative regulation of angiogenesis. Collectively, this study provides a comprehensive cross-species transcriptional profile resource for mammalian skin, providing a valuable resource for understanding the regulatory plasticity underlying skin evolution across mammals. Full article

This research focused on understanding the diversity of macrofungi in the “Tingana Conservation Concession” in San Martín, Peru, a unique flooded forest located at approximately 900 m a.s.l. in the Andean-Amazonian foothills. Three study areas were included: Sparse Aguajal, Semi-dense Aguajal, and Broadleaf Evergreen Forest. These were sampled using random transects; 19 macrofungi were identified to species level and 20 to genus level, distributed in 8 orders, 19 families, and 27 genera. The most diverse orders were Agaricales and Polyporales; the most representative families were Polyporaceae (11) and Psathyrellaceae (4). At a generic level, the most diverse was Lentinus, with a total of 5 species identified. These findings highlight the diversity and ecological importance of fungi in the decomposition of organic matter and the nutrient cycle in peatlands, which are key carbon-storing ecosystems. This study underlines the need for more research focused on inventorying fungi for the conservation of this type of ecosystem. Full article

Static Acoustic Monitoring (SAM) using C-PODs, deep C-PODs, and F-PODs was conducted as part of the STRAITS project (Strategic Infrastructure for improved animal Tracking in European Seas), funded under the EU’s Horizon research and innovation programme, to investigate odontocete acoustic occurrence across four European straits: the North Channel, the Sound, the Strait of Gibraltar, and the Dardanelles Strait. The acoustic presence of dolphin species and harbour porpoises was modelled in relation to tidal cycle, moon phase, sea surface temperature (SST), diel period, season, and Sound Pressure Levels (SPLs), representing ambient underwater sound using a Generalised Additive Modelling (GAM) approach. Harbour porpoises were primarily detected in the Sound and the North Channel, while dolphin detections were higher in the Strait of Gibraltar and the Dardanelles Strait. There was a significant association with SPLs on both species across all locations where it was assessed. There was a significant effect of tidal cycle and SST on both species across all locations except the Dardanelles Strait. Temporal patterns were significant across species and study sites. This study presents the first multi-strait assessment of odontocete occurrence in key marine corridors, highlighting the relationship of environmental and temporal drivers, underwater noise, and odontocete occurrence, and providing insights for marine spatial planning and conservation management in highly trafficked regions. Full article

Continuous monoculture in poplar plantations often leads to declining soil nutrient availability and productivity. Phosphorus (P), in particular, frequently becomes a key limiting factor due to its high fixability and low chemical availability in the soil. Understory vegetation, however, may promote soil P cycling and enhance P availability by regulating the community structure and decomposition activity of soil microorganisms. In this study, a seven-year field experiment was conducted in degraded poplar plantations using a randomized complete block design to investigate the effects of four understory vegetation treatments—understory removal (UR), planting of a nitrogen-fixing species Sesbania cannabina in understory (PN), retention of a single dominant understory species Echinochloa crus-galli (RS), and retention of diverse understory vegetation (RD)—on soil P fractions and availability, and to elucidate the microbial mechanisms driving P cycling using a metagenomic approach. The results showed that, compared with UR, all understory retention treatments significantly increased soil labile P fractions, improved microbial community structure, and enhanced the abundance of P cycling-related functional genes and associated enzyme activities. Specifically, PN enriched the bacterial phylum Chloroflexi, thereby strengthening its role in P cycling, and increased the abundance of key functional genes such as ppa and phnH. These changes led to higher activities of acid phosphatase, phosphodiesterase, and phytase, ultimately improving soil P availability. In contrast, through the input of litter with greater diversity and higher biomass, RD enriched microbial communities dominated by Proteobacteria. This treatment increased the abundance of P cycling-related genes (e.g., phnW, purK, phnP, ugpQ) and associated enzyme activities, thereby enhancing soil P mobilization. Both the introduction of nitrogen-fixing species and the increase in understory species richness promoted soil P cycling and enhanced P availability, albeit through distinct mechanisms. Planting of nitrogen-fixing species enriched specific microbial taxa and functional genes, whereas increasing understory species richness boosts P cycling by increasing bacterial species richness and functional gene abundance. Both enhancing species richness and planting nitrogen-fixing species in the understory effectively improved soil P availability and supported the sustainable management of degraded poplar plantations. Among these approaches, retaining diverse understory vegetation is more cost-effective and contributes to biodiversity conservation, making it a recommended management strategy. Full article

The UBP gene family plays a key role in various physiological processes, including cell cycle regulation, DNA repair, and stress responses. UBPs have been identified and analyzed in several species, including Moso Bamboo, Arabidopsis thaliana, Oryza sativa L., and Brachypodium distachyon. However, the UBP family within Prunus mume Siebold & Zucc. remains unexplored. In this study, 30 PmUBPs were identified and characterized, all of which contained the UCH conserved domain. They were grouped into 16 subfamilies via evolutionary analysis, revealing similarities in genome structure and motif distribution. PmUBPs were distributed on seven chromosomes and three scaffolds. Gene duplication events, including tandem duplication and segmental duplication, promoted the expansion of PmUBPs. Collinear analysis demonstrated the close relationship between P. armeniaca, P. persica, P. avium, and P. mume. Transcriptome data revealed distinct relative expression trends in PmUBP genes across different tissues. Promoter cis-acting element analysis revealed an abundance of hormone-, light-, and stress-responsive elements across all genes. Transcriptome and reverse transcription quantitative PCR (RT-qPCR) analysis showed that PmUBP2, PmUBP11, PmUBP13, PmUBP18, PmUBP22, and PmUBP26 exhibited relatively high expressions under low-temperature stress. This study provides a theoretical foundation for the role of PmUBP genes in response to low-temperature stress. Full article

Acidithiobacillus spp. are key players in metal mobilization and sulfur cycling in acidic environments, with important applications in biomining and bioleaching operations. But the evolutionary organization of the iron and sulfur oxidation systems of these organisms is not well understood. In this study, a comparative genomic analysis of 31 Acidithiobacillus genomes (95,180 predicted proteins) was performed to investigate the distribution, conservation, and genomic organization of genes involved in ferrous iron oxidation, reduced sulfur compound oxidation, respiratory electron transfer, and sulfur trafficking. This study identified key metabolic components including cyc2, rus, cyc1, petA-F, coxA-D, soxA-D, sqr, tetH, doxA, doxD, hdrA-C, tusA, and dsrE-like genes using genome annotation, conserved-domain identification, orthology inference, and gene-neighborhood analyses. The results indicate that energy metabolism in Acidithiobacillus is organized into discrete functional modules rather than as a single universally conserved pathway. The cox terminal oxidase complex and the cyc2/rus/cyc1 iron-entry modules were identified in 21 genomes (67.7%) and 19 genomes (61.3%), respectively. Sulfur associated systems displayed greater variation in gene content, Sox genes were found in 10 genomes (32.3%), SQR/TetH/Dox components in 12 genomes (38.7%), and the Hdr/Tus/DsrE sulfur-transfer system in 22 genomes (71.0%). Phylogenomic analysis revealed iron-enriched, sulfur-enriched and mixed metabolic profiles, in line with differential retention, loss and reorganization of redox modules. These results show that metabolic potential cannot be accurately predicted from single marker genes alone, but must integrate orthology, genomic context and phylogenomic relationships. This comparative genomic framework may facilitate the identification of candidate strains for biomining applications and provide insights into the potential ecological functions of Acidithiobacillus species in acidic environments. Full article

Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome shooting in staple food bamboos remain largely unknown. Here, we performed integrated metabolomic and transcriptomic analyses of Fargesia rufa rhizomes collected along an elevational gradient (1000 m, 1500 m, and 2000 m), with a critical paired comparison at 2000 m between a non-shooting cold gully-edge site (16.4 °C) and a shooting warm gully-center site (21.1 °C), where soil temperature is elevated by approximately 4 °C due to prolonged solar exposure. Our results demonstrate that soil temperature, rather than elevation per se, acts as the primary driver of rhizome shooting, with an apparent threshold near 20 °C. A core shooting metabolome (CSM) comprising 843 metabolites was consistently accumulated across all shooting conditions, which featured gibberellin/auxin precursors, TCA cycle intermediates, and phenylpropanoid compounds. Correspondingly, a core shooting transcriptome (Rh_shooting) of 10,970 genes was identified, which resolved into three functionally distinct temporal clusters: “shooting-on” (activated upon threshold crossing, enriched in hormone signaling and cell wall metabolism), “temperature-dose” (progressively upregulated with rising temperature, enriched in energy metabolism and defense), and “microenvironment-enhanced” (specifically upregulated in the high-elevation warm gully, enriched in photosynthesis and antioxidant pathways). Integrative network analysis further revealed zeatin riboside and multiple hub genes as central coordinators linking hormone signaling, energy metabolism, and cell wall remodeling. Collectively, these findings establish a molecular framework linking altitudinal temperature variation to bamboo rhizome regeneration—a process that directly determines the spatiotemporal availability of bamboo shoots for giant pandas. This work provides mechanistic insights into giant panda foraging ecology and has direct implications for predicting habitat quality under climate change and informing evidence-based conservation strategies for this flagship species and its critical food resource. Full article

Increased herbicide use in agriculture is a major threat to adjacent aquatic and wetland ecosystems. In Morocco, the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) poses a risk to temporary ponds found in agricultural landscapes. This study used mesocosm experiments to assess the effects of 2,4-D concentration (0, 0.10, 0.20, and 0.30 mg·L⁻¹) and application timing (early vs. late in the hydrological cycle) on water quality and aquatic plant communities from forest ponds not previously exposed to herbicides. At the highest concentration (0.30 mg·L⁻¹), conductivity increased from 206 to 274 µS and pH from 7.5 to 8.4 under early application. At the same time, species richness and total abundance significantly decreased with increasing 2,4-D concentrations, with the strongest effects observed under early application. Community composition shifted markedly in response to 2,4-D, with annual and submerged species showing greater sensitivity, whereas perennial and emergent species were relatively tolerant. These findings highlight the need to adopt more sustainable agricultural practices to conserve pond biodiversity. Specifically, herbicide applications should be avoided near ponds, at high application rates, and during periods early in the hydroperiod. Lastly, land-use strategies should balance agricultural productivity with the conservation of biodiversity in temporary pond ecosystems. Full article

Mangrove ecosystems store large amounts of soil organic carbon (SOC). However, degradation processes associated with invasive species can alter vegetation structure, hydrological conditions, and carbon cycling, with uncertain consequences for SOC storage and greenhouse gas emissions. This study evaluated changes in SOC stocks to 0–50 cm depth, soil CO₂, CH₄, and N₂O fluxes, and early restoration responses four years after ecological restoration in the Térraba–Sierpe National Wetland, Costa Rica. Comparisons were conducted among a conserved mangrove, a degraded mangrove dominated by Acrostichum aureum, and three restored sites subjected to hydrological rehabilitation with contrasting reforestation intensities. The degraded site showed significantly higher SOC contents (171 ± 31 Mg C ha⁻¹; p < 0.0001) compared to the conserved site (103 ± 26 Mg C ha⁻¹). CO₂ fluxes did not differ significantly between March and October. CH₄ and N₂O fluxes remained below the detection limits in most measurements. Redundancy analysis identified a significant association between vegetation composition and the measured environmental variables (p = 0.005). Higher CO₂ emissions were associated with the dominance of A. aureum. Plant density was positively related to SOC content (R² = 0.78). MR1 site, where hydrological rehabilitation was combined with high-density reforestation, had significantly higher SOC content than the degraded site (242 ± 24.3 Mg C ha⁻¹; p < 0.001). Soil CO₂ emissions at MR1 were also significantly lower than at the degraded site (p = 0.001). This study provides a pioneering field assessment of mangrove restoration through the control of A. aureum invasion. The results suggest that restoration design may influence soil carbon storage during the early stages of recovery. Full article

Assessing water quality in lotic ecosystems using biological indicators is essential for their conservation. This study analyzed the influence of physicochemical parameters (pH, conductivity, dissolved oxygen, total nitrogen, nitrates, total phosphorus, phosphates, alkalinity, and hardness) on the diversity, abundance, and distribution of protozoa at 15 sites in the upper Soto la Marina River basin, Tamaulipas, Mexico, including the Corona, Purificación, Pilón, and San Felipe rivers and the Vicente Guerrero Reservoir. Through bimonthly sampling over the annual cycle of 2021 (February–December), 24 protozoan morphospecies were identified, with dominance of Ciliophora (10 morphospecies) and Amoebozoa (4 morphospecies). Chi-square analyses revealed that morphospecies frequency was significantly dependent on sampling site (χ² = 246.72, df = 69, p < 0.001) but independent of seasonality (χ² = 0.86, df = 15, p = 1.0). Beta diversity (Sørensen–Dice index) showed low faunistic similarity among most sites (<60%), suggesting high species turnover and a local environmental filter. Using Outlying Mean Index (OMI) analysis, most morphospecies exhibited a generalist niche (low marginality, high tolerance), showing no significant relationship with the measured environmental variables. However, Vorticella sp. emerged as an exception, showing a significant association (p = 0.0329) and positive correlation with maximum pH and alkalinity values and occurring at sites with high NO₃⁻ and PO₄³⁻ concentrations, suggesting its potential as a bioindicator of organic enrichment conditions in the region. The absence of a strong environmental signal in most species underscores the complexity of these systems and the need to integrate multiple levels of bioindicators. This study provides the first baseline on the protozoan community in the area and discusses its relevance for water quality monitoring in a region of high conservation value, such as the area of influence of the Sierra de Tamaulipas. Full article

Seed longevity plays a crucial role in the persistence of plant populations, particularly in short-lived species inhabiting unpredictable environments. However, empirical data on long-term seed viability remain scarce, especially for rare and poorly known taxa. Astragalus contortuplicatus is a threatened annual species of periodically flooded habitats, characterized by sporadic occurrence and limited ecological knowledge; based on its annual life cycle and the temporal unpredictability of its habitat, its long-term population persistence is likely facilitated by persistent seed banks. In a previous study, we demonstrated that seeds of this species stored in herbarium collections can retain the ability to germinate for more than a century. Here, we reassess seed germination capacity after an additional 11.5–12 years of dry storage, using the same germination protocol, and analyse temporal changes based on repeated measurements of the same herbarium specimens. Germination data from 2014 and 2026 were evaluated using binomial models, and the relationship between seed age and germination capacity was examined using linear and non-linear approaches. Paired analyses revealed a significant overall decline in germination probability over time, although responses varied among specimens. Despite this decline, seeds from the oldest available sample (collected in 1883) still retained the ability to germinate, with 20% germination after approximately 142.5 years of storage. Across the full dataset, seed age had a significant negative effect on germination, and non-linear models provided a better fit than simple linear regression, indicating that the loss of germination capacity does not follow a strictly linear pattern. Our results confirm the exceptional longevity of seeds in this rare species while also demonstrating that germination capacity declines over time under continued dry storage. These findings are consistent with the ecological expectation that long-lived, dormant seeds may contribute to population persistence in unpredictable habitats, while underlining the potential of herbarium collections as valuable resources for the conservation and possible restoration of threatened plant species. Notably, seeds in the oldest sample retained the ability to germinate, emphasizing the exceptional longevity of seeds in this species. Full article

S-adenosyl-L-homocysteine hydrolase (SAHH) is an evolutionarily conserved enzyme present in eukaryotes, bacteria, and archaea. As the rate-limiting enzyme in the methionine cycle, it catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine, thereby modulating the S-adenosylmethionine/SAH ratio and cellular methylation potential. Dysregulation of SAHH activity is causally linked to cancer, cardiovascular disorders, and neurodegenerative conditions. This review systematically examines the biological distribution, catalytic mechanisms, structural architecture, and regulation of SAHH across diverse species. We highlight lineage-specific adaptations—including C-terminal truncation, a 40-residue substrate-binding-domain insertion, and a His-Phe molecular gate—that fine-tune substrate preference, cofactor affinity, and thermostability, with metal ions and NAD⁺ serving as key modulators of activity and conformational dynamics. These variations exemplify an evolutionary trade-off between catalytic efficiency and structural rigidity, particularly pronounced in archaeal and thermophilic orthologs. Collectively, these insights underpin the enzyme’s multifaceted translational value: SAHH serves as a therapeutic target for diverse diseases (e.g., cancer, viral infections, tuberculosis), a source of diagnostic/prognostic biomarkers (e.g., plasma homocysteine and SAH/SAM ratio), and a versatile biocatalyst for synthesizing pharmaceutical-grade adenosine and its derivatives. By integrating mechanistic, structural, and evolutionary perspectives, this review establishes a unified framework that explains these functional adaptations and their translational implications. This framework guides the rational development of SAHH-targeted inhibitors, diagnostic tools, and engineered biocatalysts, with broad applications in precision medicine and biotechnology. Full article

Largemouth bass (Micropterus salmoides) is a major aquaculture species in China. Facility-based aquaculture, such as the “168” model, a high-efficiency recirculating system using funnel-shaped ponds, has promoted water conservation and improved aquaculture efficiency through structural innovation. However, fish die sporadically as the stocking density increases with increasing fish growth. To address this issue, three density groups were established, namely, low (2.5 ± 0.5 kg/m³), medium (4.0 ± 0.5 kg/m³), and high (7.5 ± 0.5 kg/m³). Histological examinations, biochemical assays, and transcriptomic and metabolomic analyses of liver tissues were performed, and fish health was comprehensively evaluated. Histopathological analysis revealed that progressive hepatic vacuolization and severe tissue damage occurred as the fish density increased. Biochemical indicators revealed that the immune system and growth underwent compensatory activation at medium density, shifting to immune suppression, growth impairment, and hepatic exhaustion at high density. Integrated omics analysis revealed that under medium-density stress, the urea cycle was impaired; under high-density stress, Ser metabolism in the liver was rerouted, potentially to overcome methyl donor depletion and prevent disorders of polyamine metabolism, accompanied by a gradual transition from compensatory activation to functional exhaustion. These findings improve our understanding of the physiological response mechanisms of fish to high-density stress. This study provides a theoretical basis for optimizing high-density aquaculture technologies such as the “168” model. Full article

Seasonal snowpack and snowmelt are critical regulators of forest ecosystem functioning in temperate, boreal, montane, and alpine regions. Snowpack acts as a temporary water and energy reservoir, while snowmelt determines the seasonal availability of water and influences ecosystem processes during the growing season. Climate change is altering snowfall patterns, snow accumulation, and melt timing, with consequences for forest productivity, resilience, and disturbance dynamics. This review synthesizes current knowledge on snow–forest interactions and identifies major research trends, methodological approaches, and remaining knowledge gaps. The study combines a bibliometric analysis and a qualitative literature review based on publications indexed in the Scopus and Web of Science databases. A total of 695 publications were included in the bibliometric dataset and analyzed to assess temporal trends, geographical patterns, research themes, and the ecological consequences of changing snow dynamics in forests. Representative studies from this dataset were subsequently synthesized to evaluate the influence of snowpack and snowmelt on forest ecosystem functioning, resilience, and sustainability. The reviewed literature shows that snowpack and snowmelt strongly regulate forest water availability, soil thermal conditions, nutrient cycling, vegetation responses, and carbon dynamics. Changes in snow regimes, particularly reduced snow accumulation and earlier melt, can increase the risk of soil freezing, modify moisture conditions, intensify water stress, and affect ecosystem carbon balance. However, the magnitude and direction of these effects depend on forest type, species composition, climate, and landscape characteristics. Forest structure also plays an important role in controlling snow interception, accumulation, persistence, and melt processes. The bibliometric analysis indicates a rapid increase in research interest in snow–forest interactions over the last two decades, with major contributions from the United States, Canada, China, and Northern Europe. Environmental sciences, hydrology, and ecology were the dominant research areas. Despite substantial progress, uncertainties remain regarding long-term ecosystem responses, species-specific vulnerabilities, and the interactions between declining snow cover and other climate-driven disturbances. This review emphasizes that understanding snowpack and snowmelt dynamics is essential for predicting forest ecosystem responses to climate change and for improving sustainable forest management and watershed conservation strategies in snow-dependent regions. Full article

The ecological stoichiometric traits of forest floor material nutrient resorption in forest ecosystems. However, systematic insights into nutrient allocation and scaling during the transformation of plant organs to forest floor material remain limited. This study examined six representative tree species on the southern slope of the Qilian Mountains, quantifying the carbon (C), nitrogen (N), and phosphorus (P) contents and their stoichiometric characteristics in leaves, branches, and mixed forest floor material. Allometric relationships between N and P were analyzed using the standardized major axis regression. Coniferous species exhibited a conservative strategy with high C/N and C/P ratios, whereas broad-leaved species and mixed forests exhibited nutrient-enrichment strategies. During the organ-to-forest floor material transformation, N and P contents significantly reduced, whereas C/N and C/P ratios increased, indicating strong nutrient resorption. N and P were positively associated with plant organs and forest floor material, with isometric relationships (b = 1.06 and 0.98 for plant organs and forest floor material, respectively). Because the slopes did not differ significantly from 1 (p > 0.05), the N:P ratio remained relatively constant, with no significant P limitation. This indicates that tree species regulate forest floor material quality through divergent nutrient utilization strategies, modulating nutrient cycling. This study provides a theoretical foundation for the ecological restoration and stand structure optimization of alpine forests. Full article