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19 pages, 6720 KiB  
Article
Processed Pearl Millet Improves the Morphology and Gut Microbiota in Wistar Rats
by Jaqueline Maciel Vieira Theodoro, Lucimar Aguiar da Silva, Vinícius Parzanini Brilhante de São José, Nathaniel Baldwin Willis, Renata Celi Lopes Toledo, Mariana Grancieri, Carlos Wanderlei Piler Carvalho, Joseph Francis Pierre, Bárbara Pereira da Silva and Hércia Stampini Duarte Martino
Foods 2025, 14(15), 2752; https://doi.org/10.3390/foods14152752 (registering DOI) - 7 Aug 2025
Abstract
This study evaluated the effect of pearl millet subjected to different processing on the intestinal health of rats. The animals were fed a standard iron-free diet (28 days) (hemoglobin depletion: 8.65 + 1.40 g/dL of hemoglobin). Subsequently, they were divided into four groups [...] Read more.
This study evaluated the effect of pearl millet subjected to different processing on the intestinal health of rats. The animals were fed a standard iron-free diet (28 days) (hemoglobin depletion: 8.65 + 1.40 g/dL of hemoglobin). Subsequently, they were divided into four groups for hemoglobin repletion (21 days): standard diet + ferrous sulfate (SD + FS); standard diet + non-germinated open-pan cooked millet flour (SD + NGOPCMF); standard diet + germinated open-pan cooked millet flour (SD + GOPCMF); and standard diet + extrusion-cooked millet flour (SD + ECMF). Hemoglobin level did not differ among groups. The SD + NGOPCMF, SD + GOPCMF and SD + ECMF groups demonstrated a higher Chao index in the microbiome and a higher number and area of goblet cells and longitudinal muscle layer width. The SD + NGOPCMF and SD + GOPCMF groups demonstrated increased cecum weight, crypt depth, crypt thickness, and circular muscle layer width; lower fecal pH; and a higher relative abundance of Bacteroidota, while the SD + FS group showed the highest abundance of Actinobacteriota. The SD + GOPCMF group stood out for showing the lowest fecal pH, better α-diversity (Chao and Shannon index), and the highest width of the longitudinal muscle layer. In conclusion, pearl millet subjected to different processing, mainly germination, has the potential to improve the composition of the intestinal microbiota and the intestinal morphology in rats induced to iron deficiency. Full article
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29 pages, 2766 KiB  
Article
(H-DIR)2: A Scalable Entropy-Based Framework for Anomaly Detection and Cybersecurity in Cloud IoT Data Centers
by Davide Tosi and Roberto Pazzi
Sensors 2025, 25(15), 4841; https://doi.org/10.3390/s25154841 - 6 Aug 2025
Abstract
Modern cloud-based Internet of Things (IoT) infrastructures face increasingly sophisticated and diverse cyber threats that challenge traditional detection systems in terms of scalability, adaptability, and explainability. In this paper, we present (H-DIR)2, a hybrid entropy-based framework designed to detect and mitigate [...] Read more.
Modern cloud-based Internet of Things (IoT) infrastructures face increasingly sophisticated and diverse cyber threats that challenge traditional detection systems in terms of scalability, adaptability, and explainability. In this paper, we present (H-DIR)2, a hybrid entropy-based framework designed to detect and mitigate anomalies in large-scale heterogeneous networks. The framework combines Shannon entropy analysis with Associated Random Neural Networks (ARNNs) and integrates semantic reasoning through RDF/SPARQL, all embedded within a distributed Apache Spark 3.5.0 pipeline. We validate (H-DIR)2 across three critical attack scenarios—SYN Flood (TCP), DAO-DIO (RPL), and NTP amplification (UDP)—using real-world datasets. The system achieves a mean detection latency of 247 ms and an AUC of 0.978 for SYN floods. For DAO-DIO manipulations, it increases the packet delivery ratio from 81.2% to 96.4% (p < 0.01), and for NTP amplification, it reduces the peak load by 88%. The framework achieves vertical scalability across millions of endpoints and horizontal scalability on datasets exceeding 10 TB. All code, datasets, and Docker images are provided to ensure full reproducibility. By coupling adaptive neural inference with semantic explainability, (H-DIR)2 offers a transparent and scalable solution for cloud–IoT cybersecurity, establishing a robust baseline for future developments in edge-aware and zero-day threat detection. Full article
(This article belongs to the Special Issue Privacy and Cybersecurity in IoT-Based Applications)
13 pages, 2384 KiB  
Article
Legacy and Luxury Effects: Dual Drivers of Tree Diversity Dynamics in Beijing’s Urbanizing Residential Areas (2006–2021)
by Xi Li, Jicun Bao, Yue Li, Jijie Wang, Wenchao Yan and Wen Zhang
Forests 2025, 16(8), 1269; https://doi.org/10.3390/f16081269 - 3 Aug 2025
Viewed by 169
Abstract
Numerous studies have demonstrated that in residential areas of Western cities, both luxury and legacy effects significantly shape tree species diversity dynamics. However, the specific mechanisms driving these diversity patterns in China, where urbanization has progressed at an unprecedented pace, remain poorly understood. [...] Read more.
Numerous studies have demonstrated that in residential areas of Western cities, both luxury and legacy effects significantly shape tree species diversity dynamics. However, the specific mechanisms driving these diversity patterns in China, where urbanization has progressed at an unprecedented pace, remain poorly understood. In this study we selected 20 residential settlements and 7 key socio-economic properties to investigate the change trend of tree diversity (2006–2021) and its socio-economic driving factors in Beijing. Our results demonstrate significant increases in total, native, and exotic tree species richness between 2006 and 2021 (p < 0.05), with average increases of 36%, 26%, and 55%, respectively. Total and exotic tree Shannon-Wiener indices, as well as exotic tree Simpson’s index, were also significantly higher in 2021 (p < 0.05). Housing prices was the dominant driver shaping total and exotic tree diversity, showing significant positive correlations with both metrics. In contrast, native tree diversity exhibited a strong positive association with neighborhood age. Our findings highlight two dominant mechanisms: legacy effect, where older neighborhoods preserve native diversity through historical planting practices, and luxury effect, where affluent communities drive exotic species proliferation through ornamental landscaping initiatives. These findings elucidate the dual dynamics of legacy conservation and luxury-driven cultivation in urban forest development, revealing how historical contingencies and contemporary socioeconomic forces jointly shape tree diversity patterns in urban ecosystems. Full article
(This article belongs to the Section Urban Forestry)
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15 pages, 428 KiB  
Article
Biodiversity Patterns and Community Construction in Subtropical Forests Driven by Species Phylogenetic Environments
by Pengcheng Liu, Jiejie Jiao, Chuping Wu, Weizhong Shao, Xuesong Liu and Liangjin Yao
Plants 2025, 14(15), 2397; https://doi.org/10.3390/plants14152397 - 2 Aug 2025
Viewed by 487
Abstract
To explore the characteristics of species diversity and phylogenetic diversity, as well as the dominant processes of community construction, in different forest types (deciduous broad-leaved forest, mixed coniferous and broad-leaved forest, and Chinese fir plantation) in subtropical regions, analyze the specific driving patterns [...] Read more.
To explore the characteristics of species diversity and phylogenetic diversity, as well as the dominant processes of community construction, in different forest types (deciduous broad-leaved forest, mixed coniferous and broad-leaved forest, and Chinese fir plantation) in subtropical regions, analyze the specific driving patterns of soil nutrients and other environmental factors on the formation of forest diversity in different forest types, and clarify the differences in response to environmental heterogeneity between natural forests and plantation forests. Based on 48 fixed monitoring plots of 50 m × 50 m in Shouchang Forest Farm, Jiande City, Zhejiang Province, woody plants with a diameter at breast height ≥5 cm were investigated. Species diversity indices (Margalef index, Shannon–Wiener index, Simpson index, and Pielou index), phylogenetic structure index (PD), and environmental factors were used to analyze the relationship between diversity characteristics and environmental factors through variance analysis, correlation analysis, and generalized linear models. Phylogenetic structural indices (NRI and NTI) were used, combined with a random zero model, to explore the mechanisms of community construction in different forest types. Research has found that (1) the deciduous broad-leaved forest had the highest species diversity (Margalef index of 4.121 ± 1.425) and phylogenetic diversity (PD index of 21.265 ± 7.796), significantly higher than the mixed coniferous and broad-leaved forest and the Chinese fir plantation (p < 0.05); (2) there is a significant positive correlation between species richness and phylogenetic diversity, with the best fit being AIC = 70.5636 and R2 = 0.9419 in broad-leaved forests; however, the contribution of evenness is limited; (3) the specific effects of soil factors on different forest types: available phosphorus (AP) is negatively correlated with the diversity of deciduous broad-leaved forests (p < 0.05), total phosphorus (TP) promotes the diversity of coniferous and broad-leaved mixed forests, while the diversity of Chinese fir plantations is significantly negatively correlated with total nitrogen (TN); (4) the phylogenetic structure of three different forest types shows a divergent pattern in deciduous broad-leaved forests, indicating that competition and exclusion dominate the construction of deciduous broad-leaved forests; the aggregation mode of Chinese fir plantation indicates that environmental filtering dominates the construction of Chinese fir plantation; the mixed coniferous and broad-leaved forest is a transitional model, indicating that the mixed coniferous and broad-leaved forest is influenced by both stochastic processes and ecological niche processes. In different forest types in subtropical regions, the species and phylogenetic diversity of broad-leaved forests is significantly higher than in other forest types. The impact of soil nutrients on the diversity of different forest types varies, and the characteristics of community construction in different forest types are also different. This indicates the importance of protecting the original vegetation and provides a scientific basis for improving the ecological function of artificial forest ecosystems through structural adjustment. The research results have important practical guidance value for sustainable forest management and biodiversity conservation in the region. Full article
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18 pages, 4994 KiB  
Article
Plant Growth-Promoting Serratia and Erwinia Strains Enhance Tea Plant Tolerance and Rhizosphere Microbial Diversity Under Heavy Metal Stress
by Mengjiao Wang and Zhimin Xu
Agronomy 2025, 15(8), 1876; https://doi.org/10.3390/agronomy15081876 - 2 Aug 2025
Viewed by 255
Abstract
This study demonstrated that application of the particular plant growth-promoting rhizobacteria (PGPR) strains Erwinia sp. and Serratia sp. (named C15 and C20, respectively) significantly enhanced tea plant resilience in Zn (zinc)-, Pb (lead)-, and Zn + Pb-contaminated soils by the improving survival rates [...] Read more.
This study demonstrated that application of the particular plant growth-promoting rhizobacteria (PGPR) strains Erwinia sp. and Serratia sp. (named C15 and C20, respectively) significantly enhanced tea plant resilience in Zn (zinc)-, Pb (lead)-, and Zn + Pb-contaminated soils by the improving survival rates (over 60%) and chlorophyll content of tea plants, and by reducing the accumulation of these metals in tea plants’ tissues (by 19–37%). The PGPRs elevated key soil nutrients organic carbon (OC), total nitrogen (TH), hydrolysable nitrogen (HN), and available potassium (APO) and phosphorus (APH) contents. Compared to non-PGPR controls, both strains consistently increased microbial α-diversity (Chao1 index: +28–42% in Zn/Pb soils; Shannon index: +19–33%) across all contamination regimes. PCoA/UniFrac analyses confirmed distinct clustering of PGPR-treated communities, with strain-specific enrichment of metal-adapted taxa, including Pseudomonas (LDA = 6) and Bacillus (LDA = 4) under Zn stress; Rhodanobacter (LDA = 4) under Pb stress; and Lysobacter (LDA = 5) in Zn + Pb co-contamination. Fungal restructuring featured elevated Mortierella (LDA = 6) in Zn soils and stress-tolerant Ascomycota dominance in co-contaminated soils. Multivariate correlations revealed that the PGPR-produced auxin was positively correlated with soil carbon dynamics and Mortierellomycota abundance (r = 0.729), while the chlorophyll content in leaves was closely associated with Cyanobacteria and reduced by Pb accumulation. These findings highlighted that PGPR could mediate and improve in tea plant physiology, soil fertility, and stress-adapted microbiome recruitment under heavy metal contaminated soil and stress. Full article
(This article belongs to the Section Soil and Plant Nutrition)
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20 pages, 3604 KiB  
Article
Analysis of the Differences in Rhizosphere Microbial Communities and Pathogen Adaptability in Chili Root Rot Disease Between Continuous Cropping and Rotation Cropping Systems
by Qiuyue Zhao, Xiaolei Cao, Lu Zhang, Xin Hu, Xiaojian Zeng, Yingming Wei, Dongbin Zhang, Xin Xiao, Hui Xi and Sifeng Zhao
Microorganisms 2025, 13(8), 1806; https://doi.org/10.3390/microorganisms13081806 - 1 Aug 2025
Viewed by 229
Abstract
In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. [...] Read more.
In chili cultivation, obstacles to continuous cropping significantly compromise crop yield and soil health, whereas crop rotation can enhance the microbial environment of the soil and reduce disease incidence. However, its effects on the diversity of rhizosphere soil microbial communities are not clear. In this study, we analyzed the composition and characteristics of rhizosphere soil microbial communities under chili continuous cropping (CC) and chili–cotton crop rotation (CR) using high-throughput sequencing technology. CR treatment reduced the alpha diversity indices (including Chao1, Observed_species, and Shannon index) of bacterial communities and had less of an effect on fungal community diversity. Principal component analysis (PCA) revealed distinct compositional differences in bacterial and fungal communities between the treatments. Compared with CC, CR treatment has altered the structure of the soil microbial community. In terms of bacterial communities, the relative abundance of Firmicutes increased from 12.89% to 17.97%, while the Proteobacteria increased by 6.8%. At the genus level, CR treatment significantly enriched beneficial genera such as RB41 (8.19%), Lactobacillus (4.56%), and Bacillus (1.50%) (p < 0.05). In contrast, the relative abundances of Alternaria and Fusarium in the fungal community decreased by 6.62% and 5.34%, respectively (p < 0.05). Venn diagrams and linear discriminant effect size analysis (LEfSe) further indicated that CR facilitated the enrichment of beneficial bacteria, such as Bacillus, whereas CC favored enrichment of pathogens, such as Firmicutes. Fusarium solani MG6 and F. oxysporum LG2 are the primary chili root-rot pathogens. Optimal growth occurs at 25 °C, pH 6: after 5 days, MG6 colonies reach 6.42 ± 0.04 cm, and LG2 5.33 ± 0.02 cm, peaking in sporulation (p < 0.05). In addition, there are significant differences in the utilization spectra of carbon and nitrogen sources between the two strains of fungi, suggesting their different ecological adaptability. Integrated analyses revealed that CR enhanced soil health and reduced the root rot incidence by optimizing the structure of soil microbial communities, increasing the proportion of beneficial bacteria, and suppressing pathogens, providing a scientific basis for microbial-based soil management strategies in chili cultivation. Full article
(This article belongs to the Section Microbiomes)
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23 pages, 5040 KiB  
Article
Population Density and Diversity of Millipedes in Four Habitat Classes: Comparison Concerning Vegetation Type and Soil Characteristics
by Carlos Suriel, Julián Bueno-Villegas and Ulises J. Jauregui-Haza
Ecologies 2025, 6(3), 55; https://doi.org/10.3390/ecologies6030055 - 1 Aug 2025
Viewed by 192
Abstract
Our study was conducted in the Valle Nuevo National Park and included four habitat classes: tussock grass (Sabapa), pine forest (Pinoc), broadleaf forest (Boslat), and agricultural ecosystem (Ecoag). We had two main objectives: to comparatively describe millipede communities and to determine the relationships [...] Read more.
Our study was conducted in the Valle Nuevo National Park and included four habitat classes: tussock grass (Sabapa), pine forest (Pinoc), broadleaf forest (Boslat), and agricultural ecosystem (Ecoag). We had two main objectives: to comparatively describe millipede communities and to determine the relationships between population density/diversity and soil physicochemical variables. The research was cross-sectional and non-manipulative, with a descriptive and correlational scope; sampling followed a stratified systematic design, with eight transects and 32 quadrats of 1 m2, covering 21.7 km. We found a sandy loam soil with an extremely acidic pH. The highest population density of millipedes was recorded in Sabapa, and the lowest in Ecoag. The highest alpha diversity was shared between Boslat (Margalef = 1.72) and Pinoc (Shannon = 2.53); Sabapa and Boslat showed the highest Jaccard similarity (0.56). The null hypothesis test using the weighted Shannon index revealed a statistically significant difference in diversity between the Boslat–Sabapa and Pinoc–Sabapa pairs. Two of the species recorded highly significant indicator values (IndVal) for two habitat classes. We found significant correlations (p < 0.05) between various soil physicochemical variables and millipede density and diversity. Full article
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20 pages, 2782 KiB  
Article
Urban Forest Fragmentation Reshapes Soil Microbiome–Carbon Dynamics
by Melinda Haydee Kovacs, Nguyen Khoi Nghia and Emoke Dalma Kovacs
Diversity 2025, 17(8), 545; https://doi.org/10.3390/d17080545 - 1 Aug 2025
Viewed by 192
Abstract
Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of [...] Read more.
Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of 18 plots were considered in this study, with six plots for each fragment type. Intact interior forest (F), internal forest path fragment (IF), and external forest path fragment (EF) soils were sampled at 0–15, 15–30, and 30–45 cm depths and profiled through phospholipid-derived fatty acid (PLFA) chemotyping and amino sugar proxies for living microbiome and microbial-derived necromass assessment, respectively. Carbon fractionation was performed through the chemical oxidation method. Diversity indices (Shannon–Wiener, Pielou evenness, Margalef richness, and Simpson dominance) were calculated based on the determined fatty acids derived from the phospholipid fraction. The microbial biomass ranged from 85.1 to 214.6 nmol g−1 dry soil, with the surface layers of F exhibiting the highest values (p < 0.01). Shannon diversity declined systematically from F > IF > EF. The microbial necromass varied from 11.3 to 23.2 g⋅kg−1. Fragmentation intensified the stratification of carbon pools, with organic carbon decreasing by approximately 14% from F to EF. Our results show that EFs possess a declining microbiome continuum that weakens their carbon sequestration capacity in urban forests. Full article
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22 pages, 7580 KiB  
Article
Bacterial and Physicochemical Dynamics During the Vermicomposting of Bovine Manure: A Comparative Analysis of the Eisenia fetida Gut and Compost Matrix
by Tania Elizabeth Velásquez-Chávez, Jorge Sáenz-Mata, Jesús Josafath Quezada-Rivera, Rubén Palacio-Rodríguez, Gisela Muro-Pérez, Alan Joel Servín-Prieto, Mónica Hernández-López, Pablo Preciado-Rangel, María Teresa Salazar-Ramírez, Juan Carlos Ontiveros-Chacón and Cristina García-De la Peña
Microbiol. Res. 2025, 16(8), 177; https://doi.org/10.3390/microbiolres16080177 - 1 Aug 2025
Viewed by 145
Abstract
Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition [...] Read more.
Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article
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21 pages, 1538 KiB  
Article
Soil Fungal Activity and Microbial Response to Wildfire in a Dry Tropical Forest of Northern Colombia
by Eliana Martínez Mera, Ana Carolina Torregroza-Espinosa, Ana Cristina De la Parra-Guerra, Marielena Durán-Castiblanco, William Zapata-Herazo, Juan Sebastián Rodríguez-Rebolledo, Fernán Zabala-Sierra and David Alejandro Blanco Alvarez
Diversity 2025, 17(8), 546; https://doi.org/10.3390/d17080546 - 1 Aug 2025
Viewed by 193
Abstract
Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire [...] Read more.
Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire in 2014. Twenty soil samples were collected for microbiological (10 cm depth) and physicochemical (30 cm) analysis. Basal respiration was measured using Stotzky’s method, nitrogen mineralization via Rawls’ method, and fungal diversity through culture-based identification and colony-forming unit (CFU) counts. Diversity was assessed using Simpson, Shannon–Weaver, and ACE indices. The soils presented low organic matter (0.70%) and nitrogen content (0.035%), with reduced biological activity as indicated by basal respiration (0.12 kg C ha−1 d−1) and mineralized nitrogen (5.61 kg ha−1). Four fungal morphotypes, likely from the genus Aspergillus, were identified. Simpson index indicated moderate dominance, while Shannon–Weaver values reflected low diversity. Correlation analysis showed Aspergillus-3 was positively associated with moisture, whereas Aspergillus-4 correlated negatively with pH and sand content. The species accumulation curve reached an asymptote, suggesting an adequate sampling effort. Although no control site was included, the findings provide a baseline characterization of post-fire soil microbial structure and function in a dry tropical ecosystem. Full article
(This article belongs to the Section Microbial Diversity and Culture Collections)
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17 pages, 2404 KiB  
Article
Geographically Weighted Regression Enhances Spectral Diversity–Biodiversity Relationships in Inner Mongolian Grasslands
by Yu Dai, Huawei Wan, Longhui Lu, Fengming Wan, Haowei Duan, Cui Xiao, Yusha Zhang, Zhiru Zhang, Yongcai Wang, Peirong Shi and Xuwei Sun
Diversity 2025, 17(8), 541; https://doi.org/10.3390/d17080541 - 1 Aug 2025
Viewed by 209
Abstract
The spectral variation hypothesis (SVH) posits that the complexity of spectral information in remote sensing imagery can serve as a proxy for regional biodiversity. However, the relationship between spectral diversity (SD) and biodiversity differs for different environmental conditions. Previous SVH studies often overlooked [...] Read more.
The spectral variation hypothesis (SVH) posits that the complexity of spectral information in remote sensing imagery can serve as a proxy for regional biodiversity. However, the relationship between spectral diversity (SD) and biodiversity differs for different environmental conditions. Previous SVH studies often overlooked these differences. We utilized species data from field surveys in Inner Mongolia and drone-derived multispectral imagery to establish a quantitative relationship between SD and biodiversity. A geographically weighted regression (GWR) model was used to describe the SD–biodiversity relationship and map the biodiversity indices in different experimental areas in Inner Mongolia, China. Spatial autocorrelation analysis revealed that both SD and biodiversity indices exhibited strong and statistically significant spatial autocorrelation in their distribution patterns. Among all spectral diversity indices, the convex hull area exhibited the best model fit with the Margalef richness index (Margalef), the coefficient of variation showed the strongest predictive performance for species richness (Richness), and the convex hull volume provided the highest explanatory power for Shannon diversity (Shannon). Predictions for Shannon achieved the lowest relative root mean square error (RRMSE = 0.17), indicating the highest predictive accuracy, whereas Richness exhibited systematic underestimation with a higher RRMSE (0.23). Compared to the commonly used linear regression model in SVH studies, the GWR model exhibited a 4.7- to 26.5-fold improvement in goodness-of-fit. Despite the relatively low R2 value (≤0.59), the model yields biodiversity predictions that are broadly aligned with field observations. Our approach explicitly considers the spatial heterogeneity of the SD–biodiversity relationship. The GWR model had significantly higher fitting accuracy than the linear regression model, indicating its potential for remote sensing-based biodiversity assessments. Full article
(This article belongs to the Special Issue Ecology and Restoration of Grassland—2nd Edition)
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16 pages, 2820 KiB  
Article
AiiA Lactonase Suppresses ETEC Pathogenicity Through 3OC12-HSL Quenching in a Murine Model
by Yang Yang, Ji Shao, Zixin Han, Junpeng Li, Qiaoqiao Fang and Guoqiang Zhu
Microbiol. Res. 2025, 16(8), 166; https://doi.org/10.3390/microbiolres16080166 - 31 Jul 2025
Viewed by 129
Abstract
This study elucidates how the quorum-sensing (QS) signal 3OC12-HSL exacerbates enterotoxigenic E. coli (ETEC) pathogenicity and intestinal barrier dysfunction. In vitro, 3OC12-HSL enhanced ETEC C83902 growth (66.7% CFU increase at 8 h) and dysregulated stress/growth genes (e.g., eight-fold rmf upregulation under static conditions). [...] Read more.
This study elucidates how the quorum-sensing (QS) signal 3OC12-HSL exacerbates enterotoxigenic E. coli (ETEC) pathogenicity and intestinal barrier dysfunction. In vitro, 3OC12-HSL enhanced ETEC C83902 growth (66.7% CFU increase at 8 h) and dysregulated stress/growth genes (e.g., eight-fold rmf upregulation under static conditions). In synthetic gut microbiota, 3OC12-HSL selectively augmented E. coli colonization (37.6% 16S rDNA increase at 12 h). Murine studies revealed 3OC12-HSL reduced jejunal villus height (381.5 μm vs. 543.2 μm in controls), elevated serum LPS, D-lactate, and DAO, and altered microbial composition (Firmicutes/Bacteroidetes imbalance). The lactonase AiiA reversed these effects by degrading 3OC12-HSL. It abrogated bacterial growth stimulation (in vitro CFU restored to baseline), normalized microbiota diversity (Shannon index recovered to control levels), suppressed pro-inflammatory cytokines (IL-6/TNF-α reduction), and restored intestinal integrity (villus length: 472.5 μm, 20.5% increase vs. ETEC-infected mice). Our findings establish AiiA as a potent quorum-quenching agent that counteracts ETEC virulence via targeted signal inactivation, highlighting its translational value. Full article
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27 pages, 5548 KiB  
Article
Woody Vegetation Characteristics of Selected Rangelands Along an Aridity Gradient in Namibia: Implications for Rangeland Management
by Emilia N. Inman, Igshaan Samuels, Zivanai Tsvuura, Margaret Angula and Jesaya Nakanyala
Diversity 2025, 17(8), 530; https://doi.org/10.3390/d17080530 - 29 Jul 2025
Viewed by 271
Abstract
Rangelands form the ecological and economic backbone of Namibia, yet the woody plant dynamics that sustain these landscapes remain sporadically quantified across the semi-arid interior. We investigated the characteristics (stand structure, regeneration, richness, diversity, composition, ecological importance, and indicator species) of woody communities [...] Read more.
Rangelands form the ecological and economic backbone of Namibia, yet the woody plant dynamics that sustain these landscapes remain sporadically quantified across the semi-arid interior. We investigated the characteristics (stand structure, regeneration, richness, diversity, composition, ecological importance, and indicator species) of woody communities along a pronounced south-to-north rainfall gradient (85–346 mm yr−1) at five representative sites: Warmbad, Gibeon, Otjimbingwe, Ovitoto, and Sesfontein. Field sampling combined point-centered quarter surveys (10 points site−1) and belt transects (15 plots site−1). The basal area increased almost ten-fold along the gradient (0.4–3.4 m2 ha−1). Principal Coordinates Analysis (PCoA) arranged plots in near-perfect rainfall order, and Permutational Multivariate Analysis of Variance (PERMANOVA) confirmed significant site differences (F3,56 = 9.1, p < 0.001). Nanophanerophytes dominated hyper-arid zones, while microphanerophytes appeared progressively with increasing rainfall. Mean annual precipitation explained 45% of the variance in mean height and 34% of Shannon diversity but only 5% of stem density. Indicator value analysis highlighted Montinia caryophyllacea for Warmbad (IndVal = 100), Rhigozum trichotomum (75.8) for Gibeon, Senegalia senegal (72.6) for Otjimbingwe, and Senegalia mellifera (97.3) for Ovitoto. Rainfall significantly influences woody structure and diversity; however, other factors also modulate density and regeneration dynamics. This quantitative baseline can serve as a practical toolkit for designing site-specific management strategies across Namibia’s aridity gradient. Full article
(This article belongs to the Section Plant Diversity)
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21 pages, 2030 KiB  
Article
Restoring Balance: Probiotic Modulation of Microbiota, Metabolism, and Inflammation in SSRI-Induced Dysbiosis Using the SHIME® Model
by Marina Toscano de Oliveira, Fellipe Lopes de Oliveira, Mateus Kawata Salgaço, Victoria Mesa, Adilson Sartoratto, Kalil Duailibi, Breno Vilas Boas Raimundo, Williams Santos Ramos and Katia Sivieri
Pharmaceuticals 2025, 18(8), 1132; https://doi.org/10.3390/ph18081132 - 29 Jul 2025
Viewed by 553
Abstract
Background/Objectives: Selective serotonin reuptake inhibitors (SSRIs), widely prescribed for anxiety disorders, may negatively impact the gut microbiota, contributing to dysbiosis. Considering the gut–brain axis’s importance in mental health, probiotics could represent an effective adjunctive strategy. This study evaluated the effects of Lactobacillus helveticus [...] Read more.
Background/Objectives: Selective serotonin reuptake inhibitors (SSRIs), widely prescribed for anxiety disorders, may negatively impact the gut microbiota, contributing to dysbiosis. Considering the gut–brain axis’s importance in mental health, probiotics could represent an effective adjunctive strategy. This study evaluated the effects of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on microbiota composition, metabolic activity, and immune markers in fecal samples from patients with anxiety on SSRIs, using the SHIME® (Simulator of the Human Intestinal Microbial Ecosystem) model. Methods: The fecal microbiotas of four patients using sertraline or escitalopram were inoculated in SHIME® reactors simulating the ascending colon. After stabilization, a 14-day probiotic intervention was performed. Microbial composition was assessed by 16S rRNA sequencing. Short-chain fatty acids (SCFAs), ammonia, and GABA were measured, along with the prebiotic index (PI). Intestinal barrier integrity was evaluated via transepithelial electrical resistance (TEER), and cytokine levels (IL-6, IL-8, IL-10, TNF-α) were analyzed using a Caco-2/THP-1 co-culture system. The statistical design employed in this study for the analysis of prebiotic index, metabolites, intestinal barrier integrity and cytokines levels was a repeated measures ANOVA, complemented by post hoc Tukey’s tests to assess differences across treatment groups. For the 16S rRNA sequencing data, alpha diversity was assessed using multiple metrics, including the Shannon, Simpson, and Fisher indices to evaluate species diversity, and the Chao1 and ACE indices to estimate species richness. Beta diversity, which measures microbiota similarity across groups, was analyzed using weighted and unweighted UniFrac distances. To assess significant differences in beta diversity between groups, a permutational multivariate analysis of variance (PERMANOVA) was performed using the Adonis test. Results: Probiotic supplementation increased Bifidobacterium and Lactobacillus, and decreased Klebsiella and Bacteroides. Beta diversity was significantly altered, while alpha diversity remained unchanged. SCFA levels increased after 7 days. Ammonia levels dropped, and PI values rose. TEER values indicated enhanced barrier integrity. IL-8 and TNF-α decreased, while IL-6 increased. GABA levels remained unchanged. Conclusions: The probiotic combination of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 modulated gut microbiota composition, metabolic activity, and inflammatory responses in samples from individuals with anxiety on SSRIs, supporting its potential as an adjunctive strategy to mitigate antidepressant-associated dysbiosis. However, limitations—including the small pooled-donor sample, the absence of a healthy control group, and a lack of significant GABA modulation—should be considered when interpreting the findings. Although the SHIME® model is considered a gold standard for microbiota studies, further clinical trials are necessary to confirm these promising results. Full article
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24 pages, 3204 KiB  
Article
Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge
by Xiang Zeng, Jianwei Chen, Guilin Liu, Yadong Zhou, Liping Wang, Yaolei Zhang, Shanshan Liu and Zongze Shao
Biology 2025, 14(8), 954; https://doi.org/10.3390/biology14080954 - 29 Jul 2025
Viewed by 241
Abstract
Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon [...] Read more.
Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14–0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin–Benson–Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32–4.60). Its black variety scales were dominated by Campylobacterota (67.01–80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order “Endothiobacterales,” were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin–Benson–Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails’ adaptation to vent ecosystems. Full article
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