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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 (registering DOI) - 1 Aug 2025
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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18 pages, 4241 KiB  
Article
Distribution Patterns and Assembly Mechanisms of Rhizosphere Soil Microbial Communities in Schisandra sphenanthera Across Altitudinal Gradients
by Weimin Li, Luyao Yang, Xiaofeng Cong, Zhuxin Mao and Yafu Zhou
Biology 2025, 14(8), 944; https://doi.org/10.3390/biology14080944 - 27 Jul 2025
Viewed by 219
Abstract
To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 [...] Read more.
To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article
(This article belongs to the Section Ecology)
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15 pages, 1328 KiB  
Article
Effects of Ridge-Furrow Film Mulching Patterns on Soil Bacterial Diversity in a Continuous Potato Cropping System
by Shujuan Jiao, Yichen Kang, Weina Zhang, Yuhui Liu, Hong Li, Wenlin Li and Shuhao Qin
Agronomy 2025, 15(8), 1784; https://doi.org/10.3390/agronomy15081784 - 24 Jul 2025
Viewed by 217
Abstract
Soil bacteria drive biogeochemical cycles and influence disease suppression, playing pivotal roles in sustainable agriculture. Using Illumina MiSeq sequencing, we assessed how six ridge-furrow film mulching patterns affect soil bacterial diversity in a continuous potato system. The Shannon index showed significantly higher diversity [...] Read more.
Soil bacteria drive biogeochemical cycles and influence disease suppression, playing pivotal roles in sustainable agriculture. Using Illumina MiSeq sequencing, we assessed how six ridge-furrow film mulching patterns affect soil bacterial diversity in a continuous potato system. The Shannon index showed significantly higher diversity in fully mulched treatments (T2–T3) versus controls (CK), suggesting mulching enhances microbial community richness. This result suggests that complete mulching combined with ridge planting (T2) may significantly enhance bacterial proliferation in soil. The bacterial communities were predominantly composed of Acidobacteria, Pseudomonadota, Bacteroidota, Chloroflexota, and Planctomycetota. Among these, Acidobacteria showed the highest abundance, with ridge planting patterns favoring greater Acidobacteria richness compared to furrow planting. In contrast, Pseudomonadota exhibited higher abundance under half-mulching conditions than under complete mulching. At class level, Acidobacteria and Proteobacteria emerged as the most abundant groups, with Proteobacteria constituting 22.6–35.7% of total microbial populations. Notably, Proteobacteria demonstrated particular dominance under the complete mulching with ridge planting pattern (T2). At the genus level, Subgroup_6_norank represented the most dominant taxon among the 439 identified bacterial genera, accounting for 14.0–20.2% of communities across all treatments, with half-mulching ridge planting (T4) showing the highest relative abundance. Our findings demonstrate that different ridge-furrow film mulching patterns significantly influence soil microbial diversity. While traditional non-mulched (CK) and mulched flat plots (T1) exhibited similar impacts on bacterial community structure, other treatments displayed distinct taxonomic profiles. Complete mulching patterns, particularly ridge planting (T2), appear most conducive to microbial development, suggesting their potential to enhance soil biogeochemical cycling in continuous cropping systems. These results provide valuable insights for optimizing mulching practices to improve soil health in agricultural ecosystems. Full article
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20 pages, 2995 KiB  
Article
Analysis of Bacterial Community During Cow Manure and Wheat Straw Composting and the Isolation of Lignin-Degrading Bacteria from the Compost
by Hanxiang Yang, Jianguo Hu, Bingxin Zhang, Yan Li, Chenxian Yang, Fusheng Chen, Tingwei Zhu and Ying Xin
Microorganisms 2025, 13(8), 1716; https://doi.org/10.3390/microorganisms13081716 - 22 Jul 2025
Viewed by 342
Abstract
Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and [...] Read more.
Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and function in different periods of the composts were investigated. Then, bacteria with an efficient lignin degradation ability were finally screened out from the compost samples. Based on the monitoring results of the physicochemical indexes of the composting process, it was found that the temperature and pH of the compost firstly increased and then decreased with the extension of time, and the water content and C/N gradually decreased. High-throughput sequencing of compost samples from the initial (DA), high-temperature (DB), and cooling (DC) periods revealed that the number of OTUs increased sharply then stabilized around 2000, and the alpha diversity of the bacterial community decreased firstly and then increased. The predominant phyla identified included Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, determined by the relative abundance of beta-diversity-associated species. Functional gene analysis conducted using Tax4Fun revealed that the genes were primarily categorized into Metabolism, Genetic Information Processing, Environmental Information Processing, and Cellular Processes. Based on the decolorization of aniline blue and the degradation efficiency of alkali lignin, eight bacterial strains were isolated from compost samples at the three stages. Cupriavidus sp. F1 showed the highest degradation of alkali lignin with 66.01%. Cupriavidus sp. D8 showed the highest lignin degradation potential with all three enzyme activities significantly higher than the other strains. The results provide a strategy for the lignin degradation and utilization of biomass resources. Full article
(This article belongs to the Section Microbial Biotechnology)
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16 pages, 1988 KiB  
Article
The Impact of Uranium-Induced Pulmonary Fibrosis on Gut Microbiota and Related Metabolites in Rats
by Ruifeng Dong, Xiaona Gu, Lixia Su, Qingdong Wu, Yufu Tang, Hongying Liang, Xiangming Xue, Teng Zhang and Jingming Zhan
Metabolites 2025, 15(8), 492; https://doi.org/10.3390/metabo15080492 - 22 Jul 2025
Viewed by 320
Abstract
Background/Objectives: This study aimed to evaluate the effects of lung injury induced by insoluble uranium oxide particles on gut microbiota and related metabolites in rats. Methods: The rats were randomly divided into six UO2 dose groups. A rat lung injury [...] Read more.
Background/Objectives: This study aimed to evaluate the effects of lung injury induced by insoluble uranium oxide particles on gut microbiota and related metabolites in rats. Methods: The rats were randomly divided into six UO2 dose groups. A rat lung injury model was established through UO2 aerosol. The levels of uranium in lung tissues were detected by ICP-MS. The expression levels of the inflammatory factors and fibrosis indexes were measured by enzyme-linked immunosorbent assay. Paraffin embedding-based hematoxylin & eosin staining for the lung tissue was performed to observe the histopathological imaging features. Metagenomic sequencing technology and HM700-targeted metabolomics were conducted in lung tissues. Results: Uranium levels in the lung tissues increased with dose increase. The expression levels of Tumor Necrosis Factor-α (TNF-α), Interleukin-1β (IL-1β), Collagen I, and Hydroxyproline (Hyp) in rat lung homogenate increased with dose increase. Inflammatory cell infiltration and the deposition of extracellular matrix were observed in rat lung tissue post-exposure. Compared to the control group, the ratio of Firmicutes and Bacteroides in the gut microbiota decreased, the relative abundance of Akkermansia_mucinphila decreased, and the relative abundance of Bacteroides increased. The important differential metabolites mainly include αlpha-linolenic acid, gamma-linolenic acid, 2-Hydroxybutyric acid, Beta-Alanine, Maleic acid, Hyocholic acid, L-Lysine, L-Methionine, L-Leucine, which were mainly concentrated in unsaturated fatty acid biosynthesis, propionic acid metabolism, aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and other pathways in the UO2 group compared to the control group. Conclusions: These findings suggest that uranium-induced lung injury can cause the disturbance of gut microbiota and its metabolites in rats, and these changes are mainly caused by Akkermansia_mucinphila and Bacteroides, focusing on unsaturated fatty acid biosynthesis and the propionic acid metabolism pathway. Full article
(This article belongs to the Section Animal Metabolism)
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15 pages, 1589 KiB  
Article
Optimising Nature-Based Treatment Systems for Management of Mine Water
by Catherine J. Gandy, Beate Christgen and Adam P. Jarvis
Minerals 2025, 15(7), 765; https://doi.org/10.3390/min15070765 - 21 Jul 2025
Viewed by 174
Abstract
Deployment of nature-based systems for mine water treatment is constrained by system size, and the evidence suggests decreasing hydraulic conductivity (Ksat) of organic substrates over time compromises performance. In lab-scale continuous-flow reactors, we investigated (1) the geochemical and hydraulic performance [...] Read more.
Deployment of nature-based systems for mine water treatment is constrained by system size, and the evidence suggests decreasing hydraulic conductivity (Ksat) of organic substrates over time compromises performance. In lab-scale continuous-flow reactors, we investigated (1) the geochemical and hydraulic performance of organic substrates used in nature-based systems for metals removal (via bacterial sulfate reduction) from mine water, and then (2) the potential to operate systems modestly contaminated with Zn (0.5 mg/L) at reduced hydraulic residence times (HRTs). Bioreactors containing limestone, straw, and wood chips, with and without compost and/or sewage sludge all achieved 88%–90% Zn removal, but those without compost/sludge had higher Ksat (929–1546 m/d). Using a high Ksat substrate, decreasing the HRT from 15 to 9 h had no impact on Zn removal (92.5% to 97.5%). Although the sulfate reduction rate decreased at a shorter HRT, microbial analysis showed high relative abundance (2%–7%) of sulfate reducing bacteria, and geochemical modelling pointed to ZnS(s) precipitation as the main attenuation mechanism (mean ZnS saturation index = 3.91–4.23). High permeability organic substrate treatment systems operated at a short HRT may offer potential for wider deployment of such systems, but pilot-scale testing under ambient environmental conditions is advisable. Full article
(This article belongs to the Special Issue Characterization and Management of Mine Waters)
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18 pages, 2887 KiB  
Article
Effects of Natural Ingredient Xanthohumol on the Intestinal Microbiota, Metabolic Profiles and Disease Resistance to Streptococcus agalactiae in Tilapia Oreochromis niloticus
by Aiguo Huang, Yanqin Wei, Jialong Huang, Songlin Luo, Tingyu Wei, Jing Guo, Fali Zhang and Yinghui Wang
Microorganisms 2025, 13(7), 1699; https://doi.org/10.3390/microorganisms13071699 - 20 Jul 2025
Viewed by 347
Abstract
Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of [...] Read more.
Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of the natural product xanthohumol (XN) against SA infection in tilapia (Oreochromis niloticus). The results showed that XN could significantly reduce the bacterial loads of SA in different tissues (liver, spleen and brain) after treatment with different tested concentrations of XN (12.5, 25.0 and 50.0 mg/kg). Moreover, XN could improve the survival rate of SA-infected tilapia. 16S rRNA gene sequencing demonstrated that the alpha-diversity index (Chao1 and Shannon_e) was significantly increased in the XN-treated group (MX group) compared to the SA-infected group (CG group) (p < 0.05), and the Simpson diversity index significantly decreased. The Bray–Curtis similarity analysis of non-metric multidimensional scaling (NMDS) and principal coordinate analysis (PCA) showed that there were significant differences in microbial composition among groups. At the phylum level, the relative abundance of the phyla Actinobacteria, Proteobacteria and Bacteroidetes decreased in the MX group compared to the CG group, while the relative abundance of the phyla Fusobacteria, Firmicutes and Verrucomicrobia increased. Differences were also observed at the genus level; the relative abundance of Mycobacterium decreased in the MX group, but the abundance of Cetobacterium and Clostridium_sensu_stricto_1 increased. Metabolomics analysis revealed that XN changed the metabolic profile of the liver and significantly enriched aspartate metabolism, glycine and serine metabolism, phosphatidylcholine biosynthesis, arginine and proline metabolism, glutamate metabolism, urea cycle, purine metabolism, methionine metabolism, betaine metabolism, and carnitine synthesis. Correlation analysis indicated an association between the intestinal microbiota and metabolites. In conclusion, XN may be a potential drug for the prevention and treatment of SA infection in tilapia, and its mechanism of action may be related to the regulation of the intestinal microbiota and liver metabolism. Full article
(This article belongs to the Special Issue Advanced Research on Antimicrobial Activity of Natural Products)
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19 pages, 3162 KiB  
Article
Diversity and Functional Differences in Soil Bacterial Communities in Wind–Water Erosion Crisscross Region Driven by Microbial Agents
by Tao Kong, Tong Liu, Zhihui Gan, Xin Jin and Lin Xiao
Agronomy 2025, 15(7), 1734; https://doi.org/10.3390/agronomy15071734 - 18 Jul 2025
Cited by 1 | Viewed by 480
Abstract
Soil erosion-prone areas require effective microbial treatments to improve soil bacterial communities and functional traits. Understanding the driving effects of different microbial interventions on soil ecology is essential for restoration efforts. Single and combined microbial treatments were applied to soil. Bacterial community structure [...] Read more.
Soil erosion-prone areas require effective microbial treatments to improve soil bacterial communities and functional traits. Understanding the driving effects of different microbial interventions on soil ecology is essential for restoration efforts. Single and combined microbial treatments were applied to soil. Bacterial community structure was analyzed via 16S IRNA high-throughput sequencing, and functional groups were predicted using FAPROTAX. Soil microbial carbon, nitrogen, metabolic entropy, and enzymatic activity were assessed. Microbial Carbon and Metabolic Activity: The Arbuscular mycorrhizal fungi (AMF) and Bacillus mucilaginosus (BM) (AMF.BM) treatment exhibited the highest microbial carbon content and the lowest metabolic entropy. The microbial carbon-to-nitrogen ratio ranged from 1.27 to 3.69 across all treatments. Bacterial Community Composition: The dominant bacterial phyla included Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Diversity and Richness: The AMF and Trichoderma harzianum (TH) (AMF.TH) treatment significantly reduced diversity, richness, and phylogenetic diversity indices, while the AMF.BM treatment showed a significantly higher richness index (p < 0.05). Relative Abundance of Firmicutes: Compared to the control, the AMF, TH.BM, and TH treatments decreased the relative abundance of Firmicutes, whereas the AMF.TH treatment increased their relative abundance. Environmental Correlations: Redundancy and correlation analyses revealed significant correlations between soil organic matter, magnesium content, and sucrase activity and several major bacterial genera. Functional Prediction: The AMF.BM treatment enhanced the relative abundance and evenness of bacterial ecological functions, primarily driving nitrification, aerobic ammonia oxidation, and ureolysis. Microbial treatments differentially influence soil bacterial communities and functions. The AMF.BM combination shows the greatest potential for ecological restoration in erosion-prone soils. Full article
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
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13 pages, 2020 KiB  
Article
Sampling Techniques Affect Mayfly Nymph Community Indices and May Bias Bioassessments
by Zohar Yanai and Netta Dorchin
Insects 2025, 16(7), 723; https://doi.org/10.3390/insects16070723 - 16 Jul 2025
Viewed by 308
Abstract
Mayfly nymphs are reliable indicators of aquatic habitat quality, and whilst their presence and relative abundance are often used in bioassessment schemes, it is important to recognise that these attributes are affected by the sampling method employed. To test these effects, we sampled [...] Read more.
Mayfly nymphs are reliable indicators of aquatic habitat quality, and whilst their presence and relative abundance are often used in bioassessment schemes, it is important to recognise that these attributes are affected by the sampling method employed. To test these effects, we sampled stream habitats for mayflies using two commonly used techniques in a standardised setup: aquatic sweep nets and manual collection from stones. These methods resulted in different success rates in detecting certain taxa depending on their biological traits (preferred microhabitat and locomotion type). Whilst species lists generally overlapped between the two methods, they yielded different values of total abundance, taxon richness, Shannon–Wiener’s diversity index, assemblage saprobic index, and general community structure. These results suggest that reliance on a single collection method is prone to yield only partial information for ecological assessments and emphasises the importance of employing a sampling technique that is appropriate for the study question and goals or combining more than one method. Based on these findings, we outline the scientific justifications for using each sampling method. Full article
(This article belongs to the Special Issue Aquatic Insects: Ecology, Diversity and Conservation)
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15 pages, 1588 KiB  
Article
Effect of Dealcoholized Muscadine Wine on the Development of Spontaneous Colitis and Gut Microbiome in IL-10−/− Mice
by Hao Li and Liwei Gu
Nutrients 2025, 17(14), 2327; https://doi.org/10.3390/nu17142327 - 16 Jul 2025
Viewed by 324
Abstract
Background/Objectives: Colitis is a chronic condition affecting millions worldwide. Purple muscadine wine polyphenols have a unique composition and possible disease-preventive properties. This study aims to determine how dealcoholized muscadine wine (DMW) affects the development of colitis and gut microbiome in IL-10−/− [...] Read more.
Background/Objectives: Colitis is a chronic condition affecting millions worldwide. Purple muscadine wine polyphenols have a unique composition and possible disease-preventive properties. This study aims to determine how dealcoholized muscadine wine (DMW) affects the development of colitis and gut microbiome in IL-10−/− mice, compared to wild types (WT). Methods: Six-week-old male IL-10−/− and WT C57BL/6 mice were fed either a DMW-supplemented diet (4.8% v/w) or a control diet based on AIN-93M for 154 days. Colitis severity was evaluated by disease activity, intestinal permeability, gene expression of cytokines and tight junction proteins in the colon, and inflammatory cytokines in the serum. Fecal samples were collected for gut microbiome profiling via 16S rRNA gene sequencing. Results: DMW contained predominantly anthocyanins and a significant amount of ellagic acid. IL-10−/− mice developed mild colitis as indicated by the disease activity index. DMW × gene interactions decreased intestinal permeability, colonic mRNA levels of IL-1β, and serum TNF-α in the IL-10−/− mice. DMW suppressed the colonic mRNA levels of IL-6, enhanced the gene expression of ZO-1, but did not influence the mRNA level of TNF-α or occludin. While DMW did not alter α-diversity of the gut microbiome, it significantly influenced β-diversity in the WT mice. DMW significantly reduced the relative abundances of Akkermansia in the IL-10−/− and WT mice. DMW and DMW×gene interaction decreased the relative abundance of Parasutterella only in IL-10−/− mice. Conclusions: These results suggested that polyphenols from DMW interacted with genes to moderately alleviate the development of colitis in IL-10−/− mice and could be a useful dietary strategy for IBD prevention. Full article
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16 pages, 4449 KiB  
Article
Total Culturable Microbial Diversity of Food Contact Surfaces in Poultry and Fish Processing Industries After the Pre-Operational Cleaning Process
by Luiz Gustavo Bach, Gabriela Zarpelon Anhalt Braga, Márcia Cristina Bedutti, Layza Mylena Pardinho Dias, Emanoelli Aparecida Rodrigues dos Santos, Leonardo Ereno Tadielo, Evelyn Cristine da Silva, Jhennifer Arruda Schmiedt, Virgínia Farias Alves, Elaine Cristina Pereira De Martinis, Fábio Sossai Possebon, Vinicius Cunha Barcellos and Luciano dos Santos Bersot
Foods 2025, 14(13), 2387; https://doi.org/10.3390/foods14132387 - 6 Jul 2025
Viewed by 409
Abstract
This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, [...] Read more.
This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed. Full article
(This article belongs to the Section Food Microbiology)
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18 pages, 3150 KiB  
Article
Synergistic Adaptations of Yak Rumen Microbiota, Metabolites and Host to Altitudinal
by Jianming Ren, Xiong Ma, Pengfei Zhao, Lan Zhang, Shiyu Tao, Xiangyan Wang and Bingang Shi
Microorganisms 2025, 13(7), 1543; https://doi.org/10.3390/microorganisms13071543 - 30 Jun 2025
Viewed by 303
Abstract
Rumen microbiota and metabolites play important roles in energy metabolism and immune regulation in the host. However, the underlying mechanisms of their interaction with the host to regulate yak plateau adaptation remain unknown. In this study, the effects of altitude on the rumen [...] Read more.
Rumen microbiota and metabolites play important roles in energy metabolism and immune regulation in the host. However, the underlying mechanisms of their interaction with the host to regulate yak plateau adaptation remain unknown. In this study, the effects of altitude on the rumen microbiome, metabolome, and fermentation parameters of yaks were analyzed. The fiber content of pasture grasses increased with altitude, while crude protein content was significantly higher at an altitude of 2800 m (T2800) compared to an altitude of 4500 m (T4500) (p < 0.05). The acetic acid, propionic acid, and volatile fatty acids of yaks in the T4500 group were significantly higher than in the T2800 group (p < 0.05). Simpson’s index of rumen microorganisms in the T4500 group of yaks was significantly higher than in T2800 and T3500 yaks. The relative abundance of Rikenellaceae_RC9_gut_group and Succiniclasticum was significantly higher in T4500 than in T2800, while Prevotella and Streptococcus were more abundant in T2800 than in T4500. Rumen metabolomics analyses revealed that yak rumen metabolites at different altitudes were influenced by forage and altitude, mainly affecting energy metabolism and fatty acid biosynthesis (such as purine and glycerophospholipid metabolism). In summary, altitude may influence rumen microbes and metabolites through pasture nutrient composition. Full article
(This article belongs to the Special Issue Gut Bacterial Community: Competition and Mutualism)
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23 pages, 5783 KiB  
Article
Achnatherum inebrians Bacterial Communities Associated with Epichloë gansuensis Endophyte Infection Under Low-Concentration Urea Treatment: Links to Plant Growth and Root Metabolite
by Yuanyuan Jin, Zhenjiang Chen, Kamran Malik and Chunjie Li
Microorganisms 2025, 13(7), 1493; https://doi.org/10.3390/microorganisms13071493 - 26 Jun 2025
Viewed by 339
Abstract
Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. [...] Read more.
Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte–infected plants (E+) and Epichloë endophyte–free plants (E−) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E− groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO3-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E− plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E− plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E− plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth. Full article
(This article belongs to the Section Microbiomes)
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18 pages, 1697 KiB  
Article
Synergistic Effects of Organic and Chemical Fertilizers on Microbial-Mediated Carbon Stabilization: Insights from Metagenomics and Spectroscopy
by Wei Wang, Yue Jiang, Shanshan Cai, Yumei Li, Juanjuan Qu and Lei Sun
Agronomy 2025, 15(7), 1555; https://doi.org/10.3390/agronomy15071555 - 26 Jun 2025
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Abstract
Fertilization management constitutes a critical determinant of agroecosystem productivity. Reasonable fertilization can increase the organic matter content in soil; however, the potential mechanism of how different fertilization regimes impact soil carbon sequestration is unclear. We hypothesized that the combined application of biochar and [...] Read more.
Fertilization management constitutes a critical determinant of agroecosystem productivity. Reasonable fertilization can increase the organic matter content in soil; however, the potential mechanism of how different fertilization regimes impact soil carbon sequestration is unclear. We hypothesized that the combined application of biochar and organic fertilizer would enhance soil carbon sequestration by improving soil physicochemical conditions, increasing microbial activity, and promoting the accumulation of stable forms of carbon. This study systematically investigated different regimes, including the application of chemical fertilizer alone (SCN), chemical fertilizer with biochar (SCB), chemical fertilizer with organic fertilizer (SCO), and chemical fertilizer with both biochar and organic fertilizer (SCBO), on soil physiochemical properties, enzyme activities, labile organic carbon fractions, microbial carbon fixation gene expression, and community composition. The results demonstrated that (1) the application of organic materials significantly enhanced soil nutrient levels and enzyme activities, with the best performance from SCBO; (2) the organic materials increased the labile soil organic carbon (SOC) content and the carbon pool management index, with SCO showing the highest at 69.82%; (3) SCB and SCBO improved the stability of soil carbon components by increasing the proportion of Aromatic C; and (4) the carbon fixation genes ACAT and sdhA exhibited the highest abundance in SCBO. In parallel, the relative abundance of Actinomycetota increased with the application of organic materials, reaching its peak in SCBO. Mantel testing revealed a strong correlation between microbial community composition and SOC, emphasizing the importance of SOC in microbial growth and metabolism. Moreover, the strong correlation between carbon fixation genes and aromatic carbon suggested that specific carbon forms, particularly aromatic structures, played a critical role in driving microbial carbon fixation processes. Full article
(This article belongs to the Special Issue Microbial Carbon and Its Role in Soil Carbon Sequestration)
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17 pages, 1435 KiB  
Article
Effects of Cyclic Adenosine Monophosphate Nanoliposomes on Growth Performance, Gut Development and Microbiota of Broilers
by Li Chen, Li Wang, Sheng Huang, Guoqi Su, Shan Jiang, Feiyun Yang and Jingxiu Huang
Animals 2025, 15(13), 1852; https://doi.org/10.3390/ani15131852 - 23 Jun 2025
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Abstract
This study aimed to investigate the effects of Nano-cAMP on growth performance, gut development, and microbiota composition in broilers. A total of 108 21-day-old yellow-feathered female chicks were randomly divided into three groups with six replicates per group and six chicks per replicate [...] Read more.
This study aimed to investigate the effects of Nano-cAMP on growth performance, gut development, and microbiota composition in broilers. A total of 108 21-day-old yellow-feathered female chicks were randomly divided into three groups with six replicates per group and six chicks per replicate according to the principle of consistent body weight. Experimental treatments included the following: (1) CON group (basal diet), (2) cAMP group (basal diet + 0.02 g/kg cAMP), and (3) Nano-cAMP group (basal diet + 0.37 g/kg Nano-cAMP liposomes). After a 21-day experimental period, results revealed the following: Compared with the CON group, the Nano-cAMP group exhibited a significantly reduced feed-to-gain ratio (p < 0.05). The cAMP group exhibited a significant increase in duodenal index (p < 0.05), whereas the Nano-cAMP group demonstrated greater jejunal villus height (p < 0.05). Both treatment groups showed significant upregulation of cholecystokinin (CCK) and secretin gene expression (p < 0.05). Analysis of alpha-diversity indices (Chao1, Shannon, Simpson) revealed no significant differences in jejunal and cecal microbiota composition between experimental groups (p > 0.05). Notably, the relative abundance of Firmicutes significantly increased (p < 0.05) in the cAMP and Nano-cAMP groups, whereas Proteobacteria, Gemmatimonadota, and Chloroflexi significantly decreased (p< 0.05). The combined relative abundance of three Lactobacillus genera and Bifidobacterium was obviously elevated. Linear discriminant analysis identified Bifidobacterium, Ruminococcus torques group, and uncultured_Thermoanaerobacterales_bacterium as dominant genera in the intestinal tract of Nano-cAMP group. In conclusion, dietary addition of Nano-cAMP promotes jejunal development, modulates appetite hormones mRNA expression, enhances absorption capacity, increases the relative abundance of intestinal probiotics such as Bifidobacterium and cellulose-degrading bacteria such as Ruminococcus torques group, optimizes gut microbiota composition, and ultimately reduces the feed-to-gain ratio in broilers. Full article
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