Search Results (983)

The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article

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

Road density is a key indicator of human activity, causing habitat loss and fragmentation. Soil fungi, essential for ecosystem functioning, are sensitive bioindicators. Yet their responses to road density in urban green spaces are poorly characterized. Here, we analyzed the composition of the dominant fungal community, examined both the direct and indirect effects of road density on soil fungal communities, and identified specialist species. Focusing on Shanghai, China, a rapidly urbanizing city, we considered both edaphic factor and the road network. Through machine learning and Spearman correlation regression analyses, we quantified the relative importance of road density and edaphic factor in shaping fungal community composition and employed occupancy-specificity modeling to identify specialist taxa. Our results revealed that Ascomycota, Basidiomycota, Zygomycota, Rozellomycota, Chytridiomycota, and Glomeromycota were the dominant phyla, accounting for 93% of the retrieved ITS sequences. Road density was found to be the primary driver of fungal community composition, followed by soil lead and potassium concentrations. Notably, opportunistic pathogens (Acremonium spp.) correlated positively with road density (p < 0.001). Specialist species in high-density areas were primarily pathotrophic fungi, while saprotrophic fungi dominated in low-density areas. These findings highlight the need for urban planning strategies to mitigate the ecological impact of road density. Full article

Hurricanes and flooding events substantially elevate indoor fungal spore levels, which have been associated with increased risks of developing childhood asthma and other adverse respiratory outcomes. Although environmental fungal compositions following major hurricanes have been well characterized, the fungal communities within the nasal cavity (i.e., the nasal mycobiome) of exposed individuals remain unexplored. We collected nasal swab samples from infants following Hurricane Maria in San Juan, Puerto Rico, during two periods (March to August 2018 and February to September 2019). We processed a total of 58 samples (26 from the first year and 32 from the second year post-Hurricane Maria) and performed internally transcribed spacer (ITS) rRNA gene sequencing to characterize and compare the infant nasal mycobiome between the two groups. Although alpha-diversity did not differ significantly, beta-diversity analyses revealed significantly different fungal compositions between the two groups (p <0.01). Infants exposed during the first year post-Hurricane Maria had significantly higher abundances of Alternaria, Eutypella, Schizophyllum, and Auricularia, compared to infants from the second year. Alternaria was also more prevalent in the first-year than in the second-year infants (42% vs. 9%, p = 0.01). Our study provides evidence linking early-life hurricane exposures to elevated risks of developing childhood asthma. Full article

This study addresses the understanding of fungal diversity and their bioremediation roles in an integrated aquaculture wastewater bioremediation system, an area less explored compared to bacteria, viruses, and protozoa. Despite the rapid advancement and affordability of molecular tools, insights into fungal communities remain vague, and interpreting environmental studies in an ecologically meaningful manner continues to pose challenges. To bridge this knowledge gap, we developed an integrated aquaculture wastewater bioremediation system, incorporating photosynthetic bacteria, and utilizing internal transcribed spacer (ITS) sequencing to analyze fungal community composition. Our findings indicate that the fungal community in aquaculture wastewater is predominantly composed of the phyla Ascomycota and Chytridiomycota, with dominant genera including Aspergillus, Hortea, and Ciliphora. FUNGuild, a user-friendly trait and character database operating at the genus level, facilitated the ecological interpretation of fungal functional groups. The analysis revealed significant negative correlations between nutrient levels (COD_mn, NH₄⁺-N, NO₃⁻-N, NO₂⁻-N, and PO₄⁻³-P) and specific fungal functional groups, including epiphytes, animal pathogens, dung saprotrophs, plant pathogens, and ectomycorrhizal fungi. The removal rate for the COD_mn, NH₄⁺-N, NO₃⁻-N, NO₂⁻-N, and PO₄⁻³-P were 71.42, 91.37, 88.80, 87.20, and 91.72% respectively. This study highlights the potential role of fungal communities in bioremediation processes and provides a framework for further ecological interpretation in aquaculture wastewater treatment systems. Full article

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

AM fungi play a pivotal role in regulating ecosystem functioning and processes. However, the assembly of soil AM fungal communities and its drivers across Populus euphratica forests in extremely arid regions remain largely unclear. Here, we explored the composition and assembly processes of AM fungal communities in the soil of P. euphratica forests in northwest China. The results showed that soil salinity affected the composition, assembly processes, and network stability and complexity of AM fungal communities. Stochastic processes rather than deterministic processes dominated the community assembly of AM fungi. Habitat generalists were more susceptible to deterministic processes than specialists. In addition, the network analysis showed that fungal network complexity had a hump-shaped relationship with increasing soil salinity, while network stability had a U-shaped relationship. This research suggests that soil salinity plays an essential role in determining AM fungal community composition and assembly processes in P. euphratica forests of arid regions. 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

Background: Phenylketonuria (PKU) is a metabolic disorder managed through a strict, lifelong low-phenylalanine diet, which may influence gut microbiome dynamics. While gut bacterial alterations in PKU are increasingly investigated, the fungal community (mycobiome) remains largely unexplored. This study compared gut mycobiome composition and dietary profiles of paediatric PKU patients and healthy controls, stratified by age (<10 and 10–18 years). Methods: Stool samples from 20 children (10 PKU, 10 controls) were analysed using ITS1/ITS2 amplicon sequencing. Nutritional status was assessed using Body Mass Index percentiles (Polish standards), and nutrient intake was evaluated from three-day dietary records compared to national reference values. Correlations between fungal taxa and dietary factors were explored. Results: Although alpha diversity did not differ significantly, beta diversity and LEfSe analyses revealed distinct fungal profiles between PKU patients and controls, indicating a trend toward group separation (PERMANOVA: F = 1.54646, p = 0.09; ANOVA: p = 0.0609). PKU patients showed increased Eurotiales (p = 0.029), Aspergillaceae (p = 0.029), and Penicillium (p = 0.11) and decreased Physalacriaceae (0% vs. 5.84% in controls) and Malassezia (p = 0.13). Spearman’s analysis showed significant correlations between Geotrichum and intake of protein (ρ = 0.55, p = 0.0127) and phenylalanine (ρ = 0.70, p = 0.0005). Conclusions: Dietary treatment in PKU is associated with age-dependent shifts in the gut mycobiome, notably increasing the abundance of taxa such as Eurotiales, Aspergillaceae, and Penicillium, involved in carbohydrate/lipid metabolism and mucosal inflammation. These findings highlight the potential of gut fungi as nutritional and clinical biomarkers in PKU. Full article

Intercropping has been widely proven to boost agricultural yields and control diseases. This study examined the impact of sugarcane monoculture (SM) and sugarcane–pumpkin intercropping (IP) systems on soil physicochemical characteristics and microbial community dynamics. Compared to monoculture, intercropping significantly increased soil pH by 8.82% and total potassium (TK) by 17.92%, while reducing soil organic matter (SOM) by 25.56%. Bacterial communities under intercropping exhibited significantly higher alpha and beta diversity, whereas fungal community diversity remained unaffected. Notably, the relative abundances of certain taxa with known roles in plant growth promotion and pathogen suppression—such as Anaeromyxobacter, Nitrospira, and Massilia—were enriched. Canonical correlation analysis revealed that bacterial community composition was strongly associated with TK, while fungal community structure correlated with variations in soil available nitrogen (AN). These findings indicate that sugarcane–pumpkin intercropping reshapes soil microbial communities and contributes to some improvement in soil nutrient availability. Full article

Soil microbes play a crucial role in driving biogeochemical cycles and are closely linked with aboveground plants during forest succession. Moso bamboo (Phyllostachys edulis) encroachment into adjacent forests of varying composition is known to alter plant diversity in subtropical and tropical regions. However, how soil microbial communities respond to this vegetation type transformation has not fully explored. To address this knowledge gap, a time-alternative spatial method was employed in the present study, and we investigated the effect of Moso bamboo expansion into subtropical broad-leaved forest and coniferous forest on soil microbial phospholipid fatty acids (PLFAs). We also measured the dynamics of key soil properties during the Moso bamboo expansion processes. Our results showed that Moso bamboo encroachment into subtropical broad-leaved forest induced an elevation in soil bacterial PLFAs (24.78%) and total microbial PLFAs (22.70%), while decreasing the fungal-to-bacterial (F:B) ratio. This trend was attributed to declines in soil NO₃⁻-N (18.63%) and soil organic carbon (SOC) concentrations (28.83%). Conversely, expansion into coniferous forests promoted soil fungal PLFAs (40.41%) and F:B ratio, primarily driven by increases in soil pH (4.83%) and decreases in SOC (36.18%). These results provide mechanistic insights into how contrasting expansion trajectories of Moso bamboo restructure soil microbial communities and highlight the need to consider vegetation context-dependency when evaluating the ecological consequences of Moso bamboo expansion. Full article

Forests in the Eastern and Midwestern U.S. have been profoundly affected by human use over the last 150 years, with few old growth forests remaining. Such mature forests may harbor distinct communities and high biodiversity, particularly detritivores and their associated food webs. These communities, however, have been surveyed only rarely in comparisons of diversity and community composition between old and young forests. Here, we compare the mycophilous beetle communities of young and old deciduous forest stands in Southwestern Ohio (U.S.A.). We assess how the abundance and diversity of beetles associated with fungal sporocarps varies with forest age, downed woody debris, and invasive honeysuckle density. We surveyed fungus-associated beetles with baited traps at eight wooded parklands centered around Dayton, Ohio, conducting sampling three times over a growing season. In contrast to expectation, we found no clear effect of forest age on mycophilous beetle communities, but infestation by invasive honeysuckle (Lonicera maackii) negatively affected beetle abundance and diversity. Beetle abundance, richness, and community composition also strongly varied across seasonal sampling periods. Our surveys of mycophilous beetles in a Midwestern U.S. forest represent an initial step toward understanding how these communities are shaped by forest age and invasive species. Such information is crucial in managing forests to preserve biodiversity and ecosystem services. Full article

This study investigated the seasonal and spatial dynamics of off-flavour compounds—geosmin and 2-methylisoborneol (2-MIB)—in an intensive rainbow trout (Oncorhynchus mykiss) aquaculture system for human consumption in western Spain. Weekly water and fish flesh samples were collected over a 12-month period from three farms supplied by the River Tormes. Physicochemical parameters, determination of geosmin and 2-MIB by SPME-GC-MS, microbial counts, and microbial community composition were assessed alongside volatile compound concentrations. Geosmin and 2-MIB showed marked seasonal variation, with peak levels in water and fish flesh during spring and summer, correlating positively with temperature. Geosmin accumulation in fish was highest in the downstream farm, suggesting cumulative exposure effects. In contrast, 2-MIB was detected only in water and at lower concentrations. Microbial analyses revealed high bacterial and fungal diversity, including cyanobacterial taxa such as Phormidium setchellianum and Pseudoanabaena minima, known producers of geosmin and 2-MIB. These findings highlight the importance of water microbiota and environmental conditions in off-flavour development. Managing cyanobacterial populations and monitoring spatial-temporal variability are essential to mitigate the development of earthy or musty flavours and economic losses in aquaculture systems. Full article

This study aims to reveal the impact mechanisms of five typical topographic habitats in the Sanjiangyuan region (sunny slope, depression, shady slope, mountain pass, and transitional zone) on the characteristics and functions of rhizosphere soil fungal communities of Kengyilia thoroldiana, and to elucidate the association patterns between these communities and soil physicochemical factors. The species composition, diversity, molecular co-occurrence network, and FUNGuild function of microbial communities were investigated based on high-throughput sequencing technology. By combining the Mantel test and RDA analysis, the key habitat factors affecting the structure of the soil fungal community in the rhizosphere zone of Kengyilia thoroldiana were explored. The results showed that: ① The composition of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographical habitats showed significant differentiation characteristics: the number of OTUs in H2 (depression) and H5 (transitional zone) habitats was the highest (336 and 326, respectively). Habitats H2 showed a significant increase in the abundance of Ascomycota and Mortierellomycota and a significant decrease in the abundance of Basidiomycota compared to the other topographical habitats. ② The diversity and aggregation degree of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographical habitats showed differences. ③ Cluster analysis showed that the rhizosphere soil fungi in five topographical habitats of Kengyilia thoroldiana could be divided into two groups, with H2, H4 (mountain pass), and H5 habitats as one group (group 1) and H1 and H3 (shady slope) as one group (group 2). ④ The characteristics of the Kengyilia thoroldiana community and the physical and chemical properties of rhizosphere soil in five topographical habitats were significantly different, and the height, coverage, biomass, and soil nutrient content were the highest in H2 and H5 habitats, while lower in H1 and H3 habitats, with significant differences (p < 0.05). ⑤ Redundancy analysis showed that soil water content was the main driving factor to change the structure and function of the soil fungal community in the rhizosphere of Kengyilia thoroldiana in five topographic habitats in the Sanjiangyuan region. This study demonstrated that topographic habitats affected the species composition, functional pattern, and ecosystem service efficiency of the Kengyilia thoroldiana rhizosphere fungal community by mediating soil environmental heterogeneity, which provides microbial mechanistic insights for alpine meadow ecosystem protection. Full article

Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO₃⁻ levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease. Full article