Search Results (114)

Microbial communities are the fundamental determinants of Nongxiang Daqu quality. In this study, we systematically investigated the assembly and succession mechanisms of microbial communities during Nongxiang Daqu fermentation. Our findings reveal that this ecological succession is primarily driven by deterministic processes, encompassing dynamic environmental variables and interspecific microbial interactions. Significant stage-specific temporal variations in the community structure were observed, and biomarkers identified via a random forest model further corroborated these dynamic successional patterns. Both the neutral community model and Modified Stochasticity Ratio (MST) tests demonstrated that community assembly is dominated by deterministic processes, the influence of which intensifies as fermentation progresses. Notably, the fungal community exhibited a more pronounced response to these deterministic environmental selections than the bacterial community. Furthermore, co-occurrence network analysis, Mantel tests, and redundancy analysis (RDA) collectively illustrated that microbial interactions and environmental factors—specifically temperature, humidity, oxygen, carbon dioxide, and acidity—synergistically regulate this succession. Crucially, the rates of change in these environmental parameters directly dictated the pace of microbial turnover. Among these, oxygen and acidity had the greatest influence: oxygen accounted for 17.32% and 29.05% of the effects on fungi and bacteria, respectively, while acidity accounted for 16.77% and 25.23%, respectively. Time-series forecasting indicated that community structural assembly and stabilization predominantly conclude within the initial 30 days of fermentation. Ultimately, this study uncovers the ecological driving forces shaping the Nongxiang Daqu microbiome, providing a vital theoretical foundation for the targeted regulation of Daqu microecology and the enhancement of product quality. Full article

Land cover (LC) change is reshaping terrestrial ecosystems and profoundly impacting sustainable development in Africa, yet the long-term, continental-scale spatiotemporal dynamics of these shifts remain obscured. To address the above issue, this study systematically explores the spatiotemporal dynamics of LC across Africa from 1985 to 2022 by leveraging the fine-resolution remote-sensing-derived GLC_FCS30D LC dataset within a stratified Intensity Analysis framework. To decompose landscape changes into interval, category, and transition levels across five climatic sub-regions of Africa, we systematically evaluate the temporal consistency of land systems. This hierarchical approach disentangles systematic transition pathways from random fluctuations, thereby revealing the distinct regional regimes governing continental transformation of LC. Our results ultimately show a strong LC change acceleration in Africa after 2010, mainly in Southern, Eastern, and Western Africa, which together made up 80 to 90% of the continent’s LC dynamics. During the whole study period, shrubland and grassland had the highest gross turnover due to their high bidirectional volatility. Intensity-wise, forest remained inactive even though it was a persistent net loser to crop in East Africa (2010–2020), to shrub in Southern Africa (1990–2022), and to wetland in West Africa during the post-2000 intervals. Wetland had a major change in dynamics from historical growth during 1985–1990 to systematic decline in 2015–2022. Cropland increased by systematically targeting shrubland and grassland, mainly in East Africa. Additionally, the Sahel contributed 40% of continental grassland to bare area transitions, despite some recovery of grassland in the region. These findings show that aggregate net-change metrics obscure the volatility in African LC; therefore, distinct regional regimes such as agricultural expansion and forest degradation necessitate spatially differentiated management strategies. Full article

Climate change is advancing faster than conventional crop cycles, and this temporal lag represents a critical constraint on modern agricultural production. By significantly shortening generation times, speed breeding (SB) transforms breeding from a fixed constraint into a manageable experimental parameter. Today, SB is increasingly integrated within climate-smart agriculture, not only for rapid generation turnover but also through emerging stress-informed SB protocols designed to mimic key abiotic constraints. At the same time, no universal approach to SB exists. Protocols must be adapted to the highly heterogeneous species-specificities regarding photoperiodicity and light response. The accelerated loss of genetic diversity due to small populations, together with the limited ability of controlled chambers to simulate complex field conditions, remains a major challenge. This review synthesizes literature from 1995 to 2025 on the technical foundations of SB, its application in major crops, and integration with modern breeding, phenotyping, and AI-driven tools. The available knowledge and evidence indicate that SB is most effective when integrated into breeding pipelines together with multi-district field-testing and stress-aware protocols, rather than used as an isolated technique. SB provides one of the strongest levers available to accelerate crop improvement under rapidly changing climate conditions. Full article

The river ecosystems of the Qinghai–Tibet Plateau, recognized as a vital component of the “Asian Water Tower,” possess unique hydrological conditions and extreme environments that have shaped key indicator groups, most notably zooplankton. The community dynamics and structural characteristics of these zooplankton exhibit regular spatio-temporal distribution patterns across elevational gradients and seasonal successions. However, the intrinsic mechanisms underlying community succession and their correlations with environmental factors remain poorly understood, and the primary environmental drivers influencing community structure require further elucidation. Based on systematic zooplankton surveys and environmental data collection conducted across the Lhasa River basin from 2019 to 2021, this study established a comprehensive species inventory comprising 113 taxa across four major groups, alongside a multi-dimensional environmental dataset. We analyzed the spatio-temporal heterogeneities of zooplankton community structures—including abundance, biomass, and diversity indices—across different seasons and river reaches. The results revealed the composition and seasonal turnover of dominant taxa, with rotifers accounting for 39.82% of the total taxonomic richness. Mean zooplankton abundance and biomass across the basin were 1.18 ind./L and 343.60 × 10⁻⁵ mg/L, respectively, with peak values observed during autumn and within the Chabalang Wetland. The zooplankton community structure in the upstream, midstream, and downstream reaches, as well as associated wetlands, was significantly correlated with specific environmental factors (p < 0.05), including ammoniacal nitrogen (NH₄⁺-N), magnesium (Mg²⁺), total hardness (TH), potassium (K⁺), iron (Fe²⁺), sodium (Na⁺), sulfite (SO₃²⁻), nitrate ion (NO₃⁻), chloride ion (Cl⁻), total phosphorus (TP), and sulfide (S²⁻). Cl⁻, TH, Mg²⁺, SO₃²⁻, and elevation (Ele) were the key environmental drivers significantly influencing zooplankton abundance across seasons (p < 0.05). Furthermore, zooplankton abundance decreased significantly with increasing elevation during the winter. This research deepens our understanding of community assembly mechanisms in plateau river ecosystems and provides a scientific foundation for aquatic biodiversity conservation and ecological management in the Lhasa River basin. Full article

Despite the importance of surface microbiota in postharvest quality, the effects of mechanical damage on microbial succession in Hypsizygus marmoreus during refrigerated storage remain insufficiently understood. In this study, 16S rRNA gene and ITS amplicon sequencing were used to characterize the bacterial and fungal communities on intact and mechanically damaged H. marmoreus during 15 days of storage at 4 °C. Storage time, rather than mechanical damage, was the main driver of whole-community variation, although mechanical damage accelerated visible spoilage assessed qualitatively. Bacterial communities showed pronounced temporal turnover, shifting from early Firmicutes-rich assemblages to late-stage Proteobacteria-dominated communities, especially Pseudomonas. In contrast, fungal communities remained largely dominated by Ascomycota throughout storage, although mechanically damaged mushrooms showed a greater late-stage occurrence of opportunistic yeasts such as Candida. Predicted functional and phenotypic analyses further suggested late-stage increases in Gram-negative, aerobic, biofilm-forming, stress-tolerant, and potentially pathogenic bacterial traits. Because these traits were inferred from 16S rRNA gene-based prediction rather than measured directly, they should be interpreted cautiously. Overall, the results suggest that maintaining the physical integrity of H. marmoreus during postharvest handling may help preserve quality and delay the emergence of spoilage-associated microbial traits during refrigerated storage. Full article

The menstrual cycle represents a dynamic infradian rhythm characterized by coordinated fluctuations in ovarian steroids that extend beyond reproductive function and influence systemic metabolism. This narrative review synthesizes current evidence on how menstrual cycle phase modulates energy balance, macronutrient metabolism, micronutrient handling, and responses to dietary bioactive compounds. Across phases, small-to-moderate but consistent differences emerge in energy intake, resting energy expenditure, substrate utilization, and protein turnover, with a tendency toward increased energy intake and lipid oxidation during the mid-luteal phase compared with the early follicular and peri-ovulatory phases. Emerging metabolomics data further reveal coordinated cyclical variation in amino acids, B vitamins, and lipid species, suggesting temporally sensitive windows in which low energy availability or micronutrient insufficiency may more readily impair performance, recovery, or symptom burden. Importantly, menstrual cycle-related metabolic variability reflects not only estradiol and progesterone oscillations but also integrated adaptations across the hypothalamic–pituitary–adrenal axis, autonomic nervous system, immune signaling, and gut microbiota. These interconnected systems contribute to inter- and intra-individual heterogeneity in metabolic phenotype. From a clinical and applied perspective, the evidence supports “cycle-aware” but non-dogmatic nutritional strategies, particularly in contexts of metabolic dysfunction, high training loads, or reproductive disorders. Future research should systematically verify cycle phase, incorporate multi-system biomarkers, and adopt sex-specific analytical frameworks to improve translational relevance. Recognizing the menstrual cycle as a biologically meaningful metabolic variable may enhance precision nutrition, exercise prescription, and metabolic risk assessment in women. Full article

Cascade dams fragment river habitats, but how seasonal hydrology modulates the biogeography and assembly of fish gut microbiota remains unclear. We surveyed gut bacterial communities of the omnivorous fish Saurogobio punctatus across 10 reaches separated by cascade dams in the Qijiang River during the wet (summer) and dry (winter) seasons using 16S rRNA gene amplicon sequencing. Sampling was synchronized among reaches to minimize temporal variability. Winter exhibited stronger differentiation among reaches and a steeper distance–decay pattern, and reach-scale environmental heterogeneity (especially dissolved inorganic nitrogen) was more stable under weak hydrodynamics. Null model analyses showed that stochastic processes dominated in summer, with dispersal-related processes and drift being prominent under high connectivity, whereas deterministic assembly increased in winter and was mainly associated with homogeneous selection. Compositionality-aware differential abundance analysis (ANCOM-BC2) identified 409 genera with a significant seasonal differential abundance after adjusting for reach (FDR q < 0.05). Random forest classification, used as a complementary prediction-oriented feature-ranking analysis, indicated higher reach discriminability in winter, with Nitrospirota ranking among the top features. PLS-PM indicated that α-diversity had the strongest direct association with β-diversity in the specified model, whereas spatial and environmental effects were linked to β-diversity mainly through indirect, α-diversity-mediated pathways. Biologically, α-diversity may reflect an integrative summary of the within-gut taxon pool shaped by host filtering and environmentally derived inputs (e.g., diet- and habitat-associated sources), which can influence the magnitude of between-reach compositional turnover. Together, these results show that seasonal hydrological regimes tune spatial turnover and assembly of fish gut microbiota in cascade-regulated rivers. Full article

Cancer is a heterogeneous systemic disease that is strongly influenced by dynamic interactions with the tumour microenvironment (TME). Despite major advances in understanding spatial and molecular tumour heterogeneity, the temporal dynamics of tumours have received far less attention. Growing evidence has linked circadian clocks to cancer risk, progression, and treatment response, including in breast cancer. However, temporal regulation has yet to be recognized as a cancer hallmark, and its interaction with the TME remains poorly understood. This review examines how circadian rhythms organize breast cancer biology through bidirectional interactions with the TME. Circadian clocks coordinate proliferation, DNA damage responses, metabolism, and immune surveillance. Ageing, chronic stress, and obesity, all of which are established breast cancer risk modifiers, disrupt these rhythms and are reciprocally exacerbated by circadian dysfunction, establishing feed-forward loops that accelerate disease. Within the TME, the extracellular matrix (ECM) plays a central role in mediating this bidirectional control. Stiffened fibrotic stroma dampens epithelial clock amplitude, while circadian rhythms in turn shape collagen turnover and ECM remodelling. These dynamics can foster inflammation, stem cell expansion, and metastatic dissemination, including time-of-day-dependent release of circulating breast tumour cells. Systemically, circadian clocks gate immune cell trafficking, creating predictable windows of immunosurveillance and therapeutic vulnerability. By integrating insights from mechanobiology, metabolism, immune regulation, and ageing, we position circadian timing as a unifying layer that connects cell-intrinsic programmes with the evolving breast TME. Understanding these connections opens new opportunities for chronotherapeutic strategies in which treatment timing is aligned with circadian rhythms to improve outcomes. Full article

The composition, ecological network characteristics, and community assembly mechanisms of eukaryotic communities in the sediments of typical water diversion rivers (WDRs) of the Eastern Route of the South-to-North Water Diversion Project were analyzed using 18S rRNA gene sequencing during the flood and non-flood seasons. Against the backdrop of global climate change and intensified anthropogenic disturbances, shifts in hydrological regimes induced by inter-basin water transfer projects have become key factors altering the structure and function of aquatic microbial ecosystems. Clarifying the spatiotemporal dynamics and assembly mechanisms of sedimentary eukaryotic communities in water diversion rivers under different hydrological conditions is crucial for understanding the ecological response of river ecosystems to water diversion and safeguarding the ecological security of diverted water resources. The eukaryotic communities were primarily composed of Bacillariophyta, Ciliophora, Arthropoda, and Chlorophyta. The composition and distribution patterns of eukaryotic communities exhibited distinct temporal and spatial shifts under varying hydrological regimes. Stochastic dispersal was identified as the primary driver of community assembly. During the flood season, eukaryotic communities showed increased complexity, more competitive interactions, and enhanced modularity, with species turnover being the dominant structuring process. During the non-flood season, eukaryotic communities exhibited higher spatial heterogeneity. Full article

Pigs are a major source of animal protein and an important model for studying domestication, adaptation, and the genetics of complex traits. Over the past decade, pig genomics has progressed from generating reference assemblies and variant catalogues toward reconstructing population history and interpreting phenotypic divergence with greater resolution. Improvements in reference continuity, breed-matched assemblies, and pangenome/graph representations reduce reference bias in repeat-rich and structural-variant-prone regions, strengthening cross-population comparisons and fine-mapping across cohorts. Time-stratified ancient genomes provide an explicit temporal framework for evaluating lineage turnover and gene flow and support a multi-stage, network-based view of domestication. In parallel, genetic analyses of growth, carcass composition, meat quality, and disease resilience increasingly integrate association signals with regulatory annotation, gene expression, and tissue- or stage-specific context. Across these lines of work, maintaining comparability across reference frameworks remains central, including stable coordinate systems, robust imputation resources, and reproducible approaches for structural-variant genotyping. Together, these developments support more consistent inference and interpretation while providing a clearer basis for translation in breeding and biomedical research with attention to genetic diversity. Full article

Incorporating plant-based additives was a promising approach for modulating the microbial ecosystems of fermentation starters. This study investigated how adding Kuding tea (20% wt/wt) influenced the assembly and succession of fungal communities during Jiang-flavored Daqu production, compared to traditional wheat-based Daqu. Using amplicon sequencing of the ITS1 region and integrated measurements of endogenous factors, we analyzed community dynamics across a 40-day fermentation period. Results showed that tea addition significantly increased fungal diversity and altered succession trajectories. Community assembly shifted from stochastic towards deterministic processes, with homogeneous selection increasing from 0.47 in wheat-based Daqu to 0.62 in tea-added Daqu. Temporal species accumulation was stronger (STR exponent z: 0.565 vs. 0.436), while compositional turnover slowed (TDR slope w: −0.539 vs. −0.626). Random forest models revealed tea-specific fungal drivers and stronger correlations with endogenous factors (e.g., reducing sugar and moisture). We concluded that Kuding tea appears to function predominantly as an environmental filter that enhanced deterministic selection, stabilized community succession, and restructured the key microbial–physicochemical relationships, providing a potential strategy for steering Daqu fermentation. Full article

A multitemporal floristic study was conducted on the aquatic and riparian plant communities of the lower stretch of the Tiber River (central Italy) to identify any floristic changes in response to possible environmental pressures that have occurred locally over time. This investigation was carried out by comparing α- and temporal β-diversity, as well as biological, chorological, and ecological traits of plant assemblages present in permanent plots (n = 24) and sampled at two different time points (2005, 2025). Although both aquatic and riparian plant communities showed an increase in α-diversity over time (+94.1% and +56.5%, respectively), they generally exhibited different temporal patterns. The aquatic community showed a more stable floristic structure compared to the riparian one, with a persistent dominance of eutrophic and pollution-tolerant species, although local disappearance/rarefaction of some species was recorded. On the contrary, the riparian community showed greater species turnover, mainly due to an increase in generalist, ruderal and alien species, which over time have partially replaced those typically associated with riparian habitats. Ecological trait-based analyses indicated an increase over time in the percentage of thermophilous, heliophilous and nitrophilous species in both plant communities; the riparian community also showed an increase in xerophilous ones. Overall, the results indicate that aquatic and riparian communities exhibit distinct temporal dynamics within the same river system and highlight how long-term, permanent plot-based floristic monitoring is a useful tool in environmental studies. Full article

FLOCponics systems combine biofloc-based aquaculture with nutrient recycling and are considered sustainable for intensive aquaculture. However, fungal community dynamics in these systems and their links to water quality remain poorly understood. In this study, we examined temporal changes in fungal communities in a FLOCponics system-based Japanese eel aquaculture by integrating metabarcoding with weekly water quality monitoring. Electrical conductivity (EC), nitrite, and pH displayed significant temporal variation, whereas other water quality parameters remained stable. Metabarcoding yielded 217 fungal operational taxonomic units across all samples. Alpha diversity indices exhibited no significant differences among weeks, indicating stable richness and evenness. In contrast, beta diversity analyses revealed consistent temporal shifts in fungal community composition with time exerting a significant effect after accounting for tank identity. Community changes were significantly EC-associated, with associations to nitrite and nitrate. Variation partitioning indicated that time and water quality primarily explained variation through their overlapping contribution rather than independent effects. Beta diversity decomposition revealed that temporal differences were driven primarily by species replacement rather than nestedness. Environmentally responsive taxa were mainly composed of Rozellomycota, with fewer Ascomycota, including Metapochonia. These results demonstrate structured short-term temporal fungal community reassembly in FLOCponics systems and highlight fungal turnover as a potential indicator of water quality-linked microbial dynamics in sustainable aquaculture. Full article

In the past decade, non-native suckermouth armored catfish, Pterygoplichthys spp., have spread throughout the highland rivers of Lam Dong province, Vietnam. We examined spatial and temporal variation in endocrine and biochemical profiles across different river reaches, river systems, and between two sampling years (2020 and 2022). Seven blood parameters related to metabolism and energy balance were measured: total and free triiodothyronine, cholesterol, triglycerides, total protein, creatinine, and direct bilirubin. Concentrations of thyroid hormones and cholesterol did not differ significantly across sites or years. Multivariate analyses indicated that thyroid-related pathways were only weakly influenced by the environmental variation, suggesting preserved thyroid homeostasis. In contrast, triglycerides, total protein, creatinine, and direct bilirubin varied among rivers and between years at the same site, likely reflecting differences in food availability and energy balance. These results suggest that biochemical variation in non-native armored catfish is primarily expressed through lipid metabolism and protein turnover, while thyroid function remains comparatively conserved across invaded river habitats. Full article

The development of urban green infrastructures (UGI) is considered among the main nature-based solutions for climate mitigation in cities; however, the role of soils in the carbon (C) balance of UGI ecosystems remains largely overlooked. Urban green spaces are typically dominated by constructed Technosols, created by adding organic materials on top of former natural or agricultural subsoils. The combined effects of land-use history and current UGI management result in a high spatial variation of soil organic carbon (SOC) stocks and soil CO₂ emissions. Our study aimed to explore this variation for the case of Wageningen University campus. Developed on a former agricultural land, the campus area includes green spaces dominated by trees, shrubs, lawns, and herbs, with well-documented management practices for each vegetation type. Across the campus area (~32 ha), a random stratified topsoil sampling (n = 90) was conducted to map the spatial variation of topsoil (0–10 cm) SOC stocks. At the key sites (n = 8), representing different vegetation types and time of development (old, intermediate, and recent), SOC profile distribution was analyzed including SOC fractionation in surface and subsequent horizons, as well as the dynamics in soil CO₂ emissions, temperature, and moisture. Topsoil SOC contents on campus ranged from 1.1 to 5.5% (95% confidence interval). On average, SOC stocks under trees and shrubs were 10–15% higher than those under lawns and herbs. The highest CO₂ emissions were observed from soil under lawns and coincided with a high proportion of labile SOC fraction. Temporal dynamics in soil CO₂ emissions were mainly driven by soil temperature, with the strongest relation (R² = 0.71–0.88) observed for lawns. Extrapolating this relationship to the calendar year and across the campus area using high-resolution remote sensing data on surface temperatures resulted in a map of the CO₂ emissions/SOC stocks ratio, used as a spatial proxy for C turnover. Areas dominated by recent and intermediate lawns emerged as hotspots of rapid C turnover, highlighting important differences in the role of various UGI types in the C balance of urban green spaces. Full article