Search Results (327)

Sauce-flavor Daqu is the solid-state fermentation starter for sauce-flavor Baijiu. Its microbial community influences flavor formation, yet links between community change, process conditions, and flavor development during high-temperature fermentation remain unclear. We investigated Daqu fermentation by integrating high-throughput sequencing, monitoring of physicochemical parameters, and analysis of volatile compounds. Fermentation temperature showed three phases: rapid rise, fluctuating plateau, and gradual decline. High temperatures were associated with increased thermophilic microbes such as Bacillus and Thermoascus and with higher levels of reducing sugars and amino acid nitrogen; amylase, protease, and other hydrolase activities were detected. Bacterial composition varied more than fungal composition; Firmicutes and Ascomycota were the dominant phyla, and Bacillus and Thermoascus were abundant genera. Canonical correspondence analysis associated reducing sugars, acidity, and moisture with early community shifts, and amino acid nitrogen with later shifts; reducing sugars and moisture showed the strongest associations. Filamentous fungi and Bacillus correlated with pyrazine-type compounds. These results link microbial composition, process parameters, and flavor profiles, and may inform the standardization and mechanization of Daqu production. Full article

Physiographic, geographic, and environmental gradients influence the development of plant communities. This study assessed how environmental gradients affect riparian vegetation along the River Panjkora, aiming to find relationships between vegetation and abiotic factors through indicator species analysis. Vegetation was sampled using the quadrat method (1 × 1 m² for herbs, 5 × 5 m² for shrubs, 10 × 10 m² for trees), and soil samples were analyzed for edaphic variables. Indicator species and ordination analyses were performed using PCORD (version 5) and CANOCO (version 4.5) software to understand species diversity. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) identified species patterns and their links to environmental factors. A total of 216 plant species were recorded across seven stations, grouped into five communities. Community 01, Melia azedarach, Punica granatum, and Asparagus racemosus, are affected by Cr, p ≤ 0.03; Fe, p ≤ 0.01; Zn, p ≤ 0.04; and Mg, p = 0.03. On the other hand, Community 02, Populus alba, Debregeasia saeneb, and Youngia japonica, are controlled by Co, p = 0.01; pH, p = 0.03; Cd, p = 0.04; EC, p = 0.03; and TDSs, p = 0.03. The third community, with indicator species Pinus roxburghii, Rydingia limbata, and Cheilanthes pteridioides, is strongly influenced by Cr, p ≤ 0.05; Cu, p ≤ 0.03; TDSs, p = 0.02; and Zn, p = 0.03. Community 04, consisting of Ficus carica, Polygonum plebeium, and Avena sativa, is shaped by Na, p = 0.01; K, p ≤ 0.05; and Fe, p = 0.04. The fifth community, represented by Ficus palmata, Rosa multiflora, and Heliotropium europaeum, is influenced by pH, p ≤ 0.04 and Mn, p = 0.03. DCA displayed maximum gradient lengths of 6.443 (eigenvalue 0.742) on axis 1, 5.222 (0.662) on axis 2, 4.053 (0.600) on axis 3, and 4.791 (0.464) on axis 4. Soil pH, heavy metals (Cr, Fe, Zn, Mg, Co, Cd, Cu, Na, K, and Mn), EC, and TDSs were the main factors shaping community structure. The indicator species analysis is recommended to identify and conserve the rare species and native flora of a particular region. Full article

Legumes contribute to sustainable agriculture by reducing fertilizer use, enhancing nitrogen fixation, and with high species diversity (~20,000 species). Spain is a leading EU producer, yielding up to 30,000 tons of different legume varieties annually. The Mediterranean climate, particularly in regions like Andalusia, is under increasing pressure from climate change, with extreme temperature variations and drought becoming more frequent. While these changes may jeopardize crop yields, limited information is available on their effects on the nutritional profile of legumes. From 2017 to 2019, six faba bean (Vicia faba) varieties were monitored in two climatically distinct areas of Andalusia to assess the impact of temperature (T) and rainfall (R) on key nutrients and bioactive compounds, including protein, minerals (K, Ca, Mg, Zn, P, Fe, Mn, B), total polyphenol content (TPC), tannins (TA), and saponins (S). Spearman correlations showed that higher T negatively impacted TPC (r = −0.40) and Mg (r = −0.33), while positively influencing Zn (r = 0.27) and Ca (r = 0.22). Rainfall increased TPC and Mg but reduced TA, Zn, and Ca. Canonical correspondence analysis (CCA) and PERMANOVA (p < 0.001) confirmed T, R, and yield as significant factors. These insights support breeding strategies for climate-adapted, nutrient-rich faba beans and the development of more resilient food systems. Full article

Bumblebees are among the most important wild pollinators; however, their populations are declining worldwide due to factors such as climate change, habitat loss, and pesticide use. For their conservation, it is important to understand the community structure at the local scale and the drivers responsible for their assemblages. However, little is known about bumblebee community assemblages and their drivers in Yunnan Province, China. In this study, we mapped bumblebee community assemblages across 125 counties in Yunnan Province using field-collected and published data. We also quantified the climatic and land use/land cover (LULC) drivers shaping these assemblages. The climatic habitat suitability for 21 bumblebee species was assessed at the county level across Yunnan using species distribution modeling. The biogeographic zones (groups of counties) were identified using Ward’s agglomerative cluster analysis, and the impacts of 12 bioclimatic and LULC drivers on the zonation pattern were assessed using Canonical Correspondence Analysis (CCA). Results indicated that more than 70% of bumblebee species showed their highest environmental suitability in the northern region of Yunnan. Among climatic factors, temperature-related bioclimatic variables were identified as dominant drivers influencing the spatial distribution of 15 out of 21 bumblebee species within the counties of Yunnan. In contrast, five species, B. grahami, B. impetuosus, B. lepidus, B. picipies, and B. securus, showed the highest contribution from precipitation-related factors. Six biogeographic zones (I, II, III, IV, V, and VI) were identified using Ward’s agglomerative cluster analysis. All 12 drivers were found to play critical roles in shaping the community assemblages of bumblebee species. This study provides essential insights for devising targeted conservation strategies at a local scale to maintain bumblebee populations in Yunnan. Full article

Background: Streptomyces bacteria are prolific producers of secondary metabolites (SMs), including many antibiotics. However, most biosynthetic gene clusters (BGCs) remain silent under laboratory conditions. Global transcriptional regulators, such as AdpA, can activate these BGCs, but their roles in secondary metabolism are not fully understood. This study investigates the regulatory function of AdpA in Streptomyces venezuelae (AdpA_Sv), a fast-growing model species and natural chloramphenicol producer that encodes over 30 BGCs. Methods: We applied RNA-seq and ChIP-seq at 12 and 20 h—corresponding to vegetative and aerial hyphae stages—to profile the AdpA_Sv regulatory network. Results: AdpA_Sv influenced the expression of approximately 3000 genes, including those involved in primary metabolism, quorum sensing, sulfur metabolism, ABC transporters, and all annotated BGCs, and it bound to around 200 genomic sites. Integration of RNA-seq and ChIP-seq data identified a core regulon of 49–91 directly regulated genes, with additional effects likely mediated indirectly via other transcription factors or non-canonical binding sites. Motif analysis confirmed similarity to the canonical Streptomyces griseus AdpA-binding sequence, with a novel 5-bp 3′ extension. AdpA_Sv directly regulated several SM pathways, including chloramphenicol biosynthesis, potentially alleviating Lsr2-mediated repression. Conclusions: This study defines, for the first time, the direct AdpA regulon in S. venezuelae and establishes AdpA_Sv as a central regulator of secondary metabolism. Our findings highlight S. venezuelae as a promising chassis strain for heterologous expression and suggest strategies for activating silent BGCs in other Streptomyces species. Full article

Background: Edentulism, or toothlessness, is a significant public health issue with profound implications for physical and systemic health, especially during pregnancy, when hormonal and behavioral changes increase the risk of oral diseases. Indigenous populations are particularly vulnerable due to socioeconomic and cultural factors that limit access to dental care. Methods: This pilot study assessed the oral microbiota of nine women, both pregnant and non-pregnant, aged 18–35 from the Salasaca indigenous community in Ecuador, using 16S rRNA gene sequencing. Samples were collected from dentin, saliva, and oral mucosa, and analyzed for alpha and beta diversity levels, taxonomic composition, and ecological metrics using the DADA2 pipeline and a canonical correspondence analysis. Results: Pregnant participants exhibited significantly lower microbial diversity compared to non-pregnant individuals, with notable differences in species richness and community structure. Dominant phyla included Bacillota, Bacteroidota, and Pseudomonadota. Prevotella sp., Neisseria sp., and Haemophilus sp. were among the prevalent genera, with the canonical correspondence analysis highlighting associations between microbial profiles and variables such as gestational status, marital status, and BMI. Conclusion: The findings suggest that pregnancy influences the oral microbiota composition, potentially predisposing women to dysbiosis and dental pathology. This study highlights the need for targeted oral health strategies during pregnancy and serves as a foundation for larger studies in underserved indigenous populations. Full article

The combined effects of anthropogenic activities and climate change, particularly the increasing frequency of extreme rainfall events, continue to pose significant threats to the security of reservoir ecosystems and water quality. Effective prediction and management of aquatic ecosystems require a comprehensive understanding of how environmental factors influence the dynamics of phytoplankton communities. However, the response patterns of phytoplankton community diversity, niche breadth, and cell density to rainfall disturbances in complex mountainous riverine reservoirs remain poorly understood. In this study, we systematically investigated the phytoplankton community structure and its environmental drivers in Zhaoshandu Reservoir (China) via field surveys, morphological identification of samples, and multivariate statistical analyses. Water temperature (WT), rainfall, and phytoplankton cell density in the study area ranged from 11.4 °C to 35.6 °C, from 0 to 72.5 mm, and from 3.33 × 10³ to 7.95 × 10⁷ cells/L, respectively. Total phosphorus and total nitrogen concentrations ranged from 0.002 to 0.633 mg/L and from 0.201 to 5.06 mg/L, respectively. Canonical correspondence analysis found that rainfall and WT were the pivotal drivers of phytoplankton density and biomass and were significantly correlated with phytoplankton diversity. Importantly, structural equation modeling revealed that the direct effects of both rainfall and WT on phytoplankton diversity and niche width, as well as the indirect effects of rainfall on ammonium nitrogen concentration, significantly modulated algal density and biomass in Zhaoshandu Reservoir. Our study highlights the role of rainfall as a potential major regulator of phytoplankton communities in this riverine reservoir. Full article

Managed freshwater replenishment is a significant restoration method in the Yellow River Delta. However, their impacts on plankton communities, which are key bioindicators of aquatic ecosystem health and sensitive to the changes in the environment, remain poorly quantified. In this study, we conducted plankton surveys across wetlands subjected to freshwater restoration durations ranging from 5 to 22 years. We assessed shifts in phytoplankton and zooplankton community structure, biomass, diversity, and their relationships with environmental drivers. Results revealed distinct temporal dynamics: phytoplankton biomass and diversity followed a “U-shaped” trajectory (initial decline followed by recovery), while zooplankton biomass decreased but diversity increased with restoration duration. Canonical Correspondence Analysis (CCA) and Partial Least Squares Path Modeling (PLS-PM) identified salinity (Cl⁻, SO₄²⁻) and dissolved nitrate (NO₃⁻) as primary environmental controls for both groups. Cyanobacteria dominated phytoplankton biomass initially but declined with restoration age, while rotifers replaced copepods as the dominant zooplankton taxon over time. These findings demonstrate that freshwater restoration restructures plankton communities through salinity-mediated physiological constraints and altered nutrient availability, with implications for ecosystem function and adaptive management in anthropogenically influenced deltas. Full article

In the present scenario, coherent states of a quantum harmonic oscillator are generalized with positive Fox H auxiliary functions. The novel generalized coherent states provide canonical coherent states and Mittag-Leffler or Wright generalized coherent states, as particular cases, and resolve the identity operator, over the Fock space, with a weight function that is the product of a Fox H function and a Wright generalized hypergeometric function. The novel generalized coherent states, or the corresponding truncated generalized coherent states, are characterized by anomalous statistics for large values of the number of excitations: the corresponding decay laws exhibit, for determined values of the involved parameters, various behaviors that depart from exponential and inverse-power-law decays, or their product. The analysis of the Mandel Q factor shows that, for small values of the label, the statistics of the number of excitations becomes super-Poissonian, or sub-Poissonian, by simply choosing sufficiently large values of one of the involved parameters. The time evolution of a generalized coherent state interacting with a thermal reservoir and the purity are analyzed. Full article

Background: Centromeric alpha satellite DNA is organized into higher-order repeats (HORs), whose precise structure is often difficult to resolve in standard genome assemblies. The recent telomere-to-telomere (T2T) assembly of the human genome enables complete analysis of centromeric regions, including the full structure of HOR arrays. Methods: We applied the novel high-precision GRMhor algorithm to the complete T2T-CHM13 assembly of human chromosome 21. GRMhor integrates global repeat map (GRM) and monomer distance (MD) diagrams to accurately identify, classify, and visualize HORs and their subfragments. Results: The analysis revealed a novel Cascading 11mer HOR array, in which each canonical HOR copy comprises 11 monomers belonging to 10 different monomer types. Subfragments with periodicities of 4, 7, 9, and 20 were identified within the array. A second, complex 23/25mer HOR array of mixed Willard’s/Cascading type was also detected. In contrast to the hg38 assembly, where a dominant 8mer and 33mer HOR were previously annotated, these structures were absent in the T2T-CHM13 assembly, highlighting the limitations of hg38. Notably, we discovered a novel 52mer HOR—the longest alpha satellite HOR unit reported in the human genome to date. Several subfragment repeats correspond to alphoid subfamilies previously identified using restriction enzyme digestion, but are here resolved with higher structural precision. Conclusions: Our findings demonstrate the power of GRMhor in resolving complex and previously undetected alpha satellite architectures, including the longest canonical HOR unit identified in the human genome. The precise delineation of superHORs, Cascading structures, and HOR subfragments provides unprecedented insight into the fine-scale organization of the centromeric region of chromosome 21. These results highlight both the inadequacy of earlier assemblies, such as hg38, and the critical importance of complete telomere-to-telomere assemblies for accurately characterizing centromeric DNA. Full article

Reductive soil disinfestation (RSD) significantly alters soil characteristics, yet its combined effects with bacterial inoculation on subsequent rhizospheric microbial community composition remains poorly understood. To address this knowledge gap, we investigated the effects of RSD and endophytic Brevibacillus laterosporus inoculation on the composition, network, and predicted function of peanut rhizospheric bacteria and fungi. Our results demonstrated that RSD and B. laterosporus inoculation substantially increased rhizospheric bacterial diversity while reducing fungal diversity. Specifically, B. laterosporus-enhanced RSD significantly reshaped the bacterial community, resulting in increased relative abundances of Chloroflexi, Desulfobacterota, and Myxococcota while decreasing those of Firmicutes, Gemmatimonadota, and Acidobacteriota. The fungal community exhibited a more consistent response to RSD and B. laterosporus amendment, with reduced proportions of Ascomycota and Gemmatimonadota but an increase in Chytridiomycota. Network analysis revealed that B. laterosporus inoculation and RSD enhanced the bacterial species complexity and keystone taxa. Furthermore, canonical correspondence analysis indicated strong associations between the soil bacterial community and soil properties, including Eh, EC, NO₃⁻-N, and SOC. Our findings highlight that the shifts in bacterial taxa induced by B. laterosporus inoculation and RSD, particularly the keystone taxa identified in the network, may contribute to the suppression of soil-borne pathogens. Overall, this study provides a novel insight into the shifts in rhizospheric bacterial and fungal communities and their ecological functions after bacteria inoculation and RSD treatment. Full article

To accurately assess the water quality, ecosystem status, distribution of large benthic organisms, and ecological restoration under human intervention, an analysis of benthic organisms on Caofeidian in September and November 2023 and January and May of the following year was conducted in this work. By performing CCA (canonical correspondence analysis) and cluster and correlation coefficient (Pearson) analyses, the temporal variation characteristics of benthic abundance, dominant species, community structure and biodiversity were analyzed. A total of 79 species of macro-benthic animals were found in four months, including 32 species of polychaetes, cnidarians, 1 species of Nemertean, 19 species of crustaceans, and 24 species of molluscs. The use of conventional grab-type mud collectors revealed that the Musculus senhousei dominated the survey (Y > 0.02). While only a small number of Ruditapes philippinarum were collected from bottom-dwelling species, a certain number of bottom-dwelling species (Ruditapes philippinarum and Scapharca subcrenata) were also collected during the trawl survey. Additionally, a significant population of Rapana venosa was found in the area. It is speculated that the dual effects of predation and competition are likely the primary reasons for the relatively low abundance of bottom-dwelling species. The density and biomass of macro-benthos were consistent over time, which was the highest in May, the second highest in January, and the lowest in September and November. The main environmental factors affecting the large benthic communities in the surveyed sea areas were pH, DO, NO₂⁻-N, T, SAL and PO₄³⁻-P. Combined with historical data, it was found that although the environmental condition in the Caofeidian sea area has improved, the Musculus senhousei has been dominant. In addition, the abundance of other species is much less than that of the Musculus senhousei, and the diversity of the benthic community is still reduced. Our work provides valuable data support for the management and improvement of bottom Marine pasture and promotes the transformation of Marine resources from resource plunder to a sustainable resource. Full article

This study investigates the mechanisms of zooplankton community assembly and their relationship to environmental factors in high-latitude arid regions. We conducted seasonal sampling at four reservoirs in the upper Tarim River Basin from 2023 to 2024: Shangyou Reservoir (SY), Shengli Reservoir (SL), Duolang Reservoir (DL) and Xinjingzi Reservoir (XJZ). The zooplankton community was categorized into five functional groups based on the predominant species, with small crustacean filter feeders (SCF) in all reservoirs except XJZ, where a seasonal shift between rotifer collectors (RC) in the wet season and SCF in the dry season was observed. Pearson correlation and canonical correspondence analysis (CCA) revealed that interspecific competition, pH, conductivity (COND), and salinity (SALIN) were the main determinants of zooplankton community composition. Significant correlations (p < 0.05) were detected among functional groups RC (rotifers carnivora), RF (rotifers filter feeders), SCF (small copepods and claocera filter feeders), and MCC (middle copepods and claocera carnivora). Environmental factors showed significant spatial heterogeneity, while zooplankton biomass was positively correlated with pH and COND. Cluster similarity analyses indicated complex interactions between 29 zooplankton species, with RF identified as an important positive predictor for larger groups. The network of co-occurrences showed predominantly positive relationships, emphasizing the mutual facilitation between the species. Our results suggest that interspecific interactions have stronger effects on community structuring than environmental factors, with mutual facilitation emerging as an important survival strategy. This study provides important insights into the dynamics of zooplankton communities in dry reservoirs and establishes a framework for understanding ecological patterns and assembly mechanisms under drought conditions. Full article

Despite Qatar’s depressions being ecologically significant for biodiversity in arid desert regions, they remain poorly studied. This study aimed at assessing the floristic diversity of Qatar’s depression habitat and examining the key environmental drivers shaping vegetation patterns. We applied multivariate analyses, including Canonical Correspondence Analysis (CCA) and Two-Way Indicator Species Analysis (TWINSPAN), to understand the environmental factors that shape vegetation communities and classify the depression sites. A total of 139 plant species from 35 families were recorded from 26 depression sites across Qatar. Both therophytes and chamaephytes were the dominant life forms. Biregional chorotypes were the most prevalent among phytogeographical groups. CCA indicated that grazing pressure, latitude, nitrogen concentration, clay content, and soil pH were among the variables that influenced the vegetation patterns of depressions, while longitude and soil carbon content showed marginal significance in explaining the observed floristic variation. TWINSPAN classified the sites into four distinct clusters, each associated with specific indicator species and habitat conditions. Northern depressions supported higher species richness compared to central and southern depressions, which are dominated by sandy soils and experience intensive grazing patterns that reduce the floristic diversity and limited regeneration of key shrubs such as Vachellia tortilis (Forssk.) Galasso & Banfi. This study helps fill a critical knowledge gap about Qatar’s depression habitat, enhancing efforts to conserve these vulnerable ecosystems, identify ecological threats, and better understand patterns of species distribution across arid landscapes. Full article

This study explored the beta diversity patterns of tenebrionid beetles and their driving factors across four grassland types in Ningxia. A total of 32 monitoring sites were surveyed, capturing 5328 individuals from 47 tenebrionid species. Permutation multivariate dispersion (PERMDISP) and non-metric multidimensional scaling (NMDS) revealed significant differences in community composition among the four grassland types (Stress = 0.091). Beta diversity decomposition indicated that species replacement primarily drives beta diversity among four temperate grassland types. Canonical Correspondence Analysis (CCA) showed that mean temperature, field water holding capacity, total soil phosphorus, biomass of Asteraceae, biomass of Leguminosae, and frequency of Leguminosae significantly explained variations in dominant species abundance (p < 0.05). Mantel tests revealed that beta diversity was positively correlated with differences in mean temperature, field water holding capacity, total soil phosphorus, and Asteraceae biomass (p < 0.01), but negatively correlated with Leguminosae frequency (p < 0.05). Overall, daily mean temperature was the primary driver of diversity, with synergistic effects from climate, elevation, soil, and vegetation. This study provides a comprehensive analysis of environmental factors influencing tenebrionid diversity, offering insights for grassland biodiversity conservation. Full article