Search Results (153)

Constructed wetlands (CWs) are widely used for ecological restoration, but their microbial assembly mechanisms and ecological functions remain poorly understood, limiting the optimization of restoration strategies. In this study, we investigated foliar fungal communities associated with dominant plant types in a CW converted from farmland by employing high-throughput sequencing. We analyzed community composition, diversity, assembly processes, and co-occurrence network structure to identify potential keystone taxa. Our results showed that plant type significantly influenced fungal community diversity and composition (α < 0.05). Assembly processes were jointly driven by heterogeneous selection (36.48%), dispersal-related processes (35.49%), and drift (24.70%), indicating comparable contributions of deterministic and stochastic processes. Co-occurrence network analysis revealed a modular structure and identified several hub taxa based on topological indices, suggesting their potential importance for network stability. This study provides an integrated perspective that links community diversity, assembly mechanisms, and network structure, providing insights for improving CW vegetation management and microbial regulation strategies. Future studies should explore and validate the functional roles of hub taxa and test the generalizability of these patterns across multiple regions and seasons. Full article

Although bacterial and fungal communities play essential roles in organic matter degradation and humification during composting, their composition, interactions, abiotic compost properties, and succession patterns remain unclear. In this study, the succession of bacterial and fungal communities during algal sludge composting was explored using 16S and ITS rRNA amplicon sequencing. The compost rapidly entered the thermophilic phase (>50 °C) within the first phase. During the composting process, the diversity of bacterial and fungal communities did not show a significant response to the different composting phases. The physicochemical parameters and microbial community structures changed significantly during the thermophilic and cooling phases, particularly in the former, and gradually stabilized as the compost matured. Integrated random forest and network analyses suggested that the bacteria genera Geobacillus and Parapedobacter, along with the fungus genus Gilmaniella, could serve as potential biomarkers for different composting phases. The functional activity of the bacterial communities was obviously higher during the thermophilic phase than during the other phases, while fungal activity remained relatively high during both the thermophilic and cooling phases. Structural Equation Modeling (SEM) further indicated that bacterial communities primarily mediated nitrogen transformation and humification processes, while fungal communities mainly contributed to humification. These results cast a new light on understanding about microbial function during aerobic algal sludge composting. Full article

Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article

In view of the increasing environmental pollution caused by bisphenol A (BPA), understanding its impact on the microbiological properties of soil, which play a key role in maintaining soil fertility and consequently ecosystem stability, is particularly important. Therefore, the aim of this study was to assess the sensitivity of the soil microbiome to this xenobiotic and to evaluate the potential of organic materials such as starch (St), grass compost (Co), and fermented bark (B) to restore the balance of soil cultivated with Zea mays. The negative effects of BPA on the abundance, diversity, and structure of bacterial and fungal communities in soil contaminated with 500 and 1000 mg kg⁻¹ d.m. of soil were confirmed. Changes in the phospholipid profile, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and ergosterol (E), were also assessed. BPA applied at 1000 mg kg⁻¹ d.m. of soil inhibited the proliferation of organotrophic bacteria and actinomycetes, while stimulating fungal growth. This xenobiotic’s impact is also reflected by a decrease in PC and PG levels in soil under BPA pressure. Through amplification of the V3-V4 16S rRNA region (for bacteria) and the ITS1 region (for fungi), the dominant bacterial phylum Proteobacteria was identified, with genera including Cellulosimicrobium, Caulobacter, Rhodanobacter, Sphingomonas, Mucilaginibacter, and Pseudomonas. Among fungi, Ascomycota dominated, primarily represented by the genus Penicillium. Of all the organic materials tested for mitigating BPA’s negative effects, grass compost was identified as the most promising, not only restoring soil homeostasis but also enhancing the growth and development of Zea mays cultivated in BPA-contaminated soil. Full article

Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing to assess the ecological impacts of two polyculture methods involving river crabs on sediment bacteria, fungi, and protists. One method involved polyculturing river crabs with mandarin fish, silver carp, and the stone moroko (SPC), and the other involved polyculturing river crabs with only mandarin fish and silver carp (SMC). The results showed that, compared to the SMC group, the SPC group remarkably increased the Chao1 index of bacterial communities in pond sediment and decreased the Pielou_J index of protists. The relative abundances of all fungal phyla and most dominant bacterial and protistan phyla (top 10 in relative abundance) in the SPC group were considerably different from those in the SMC group. In the co-occurrence networks of bacterial, fungal, and protistan communities, the numbers of edges and nodes were higher in the SPC group than in the SMC group, and the habitat niche breadth of bacterial community was also notably increased in the SPC group. The levels of total carbon (TC), total nitrogen (TN), and phosphates within pond sediment in the SPC group were obviously lower than those in the SMC group, and were significantly correlated with the microbial communities, with TC being identified as the primary contributor driving changes in the microbial communities. All the findings collectively demonstrate that the polyculture of river crabs with mandarin fish, silver carp, and the stone moroko enhances the stability of bacterial, fungal, and protistan communities in sediment and enhances resource utilization efficiency in aquaculture, thereby preventing the environmental risks associated with excessive nutrient accumulation in sediment. Polyculture systems integrating river crabs with mandarin fish, silver carp, and the stone moroko represent a sustainable aquaculture model with significant ecological benefits. Full article

Calcium (Ca) is one of the most important elements determining vegetable yield, but the driving factors that regulate microbial community structure, microbial network system stability, and metabolic pathways along the soil Ca gradient remain unclear. In this work, the relationship between soil physicochemical properties and bacterial and fungal communities was investigated under distinct Ca gradients in well-established Chinese cabbage fields located in Shijiazhuang, Hebei Province, China, with sites named Group 1 (G1), Group 2 (G2), and Group 3 (G3) from lowest to highest along the soil Ca gradient. This study demonstrated that Ca exerts dual effects by modulating pH, electrical conductivity (EC), and soil organic carbon (SOC) dynamics, enhancing bacterial diversity while reinforcing fungal network stability through distinct metabolic adaptations. Bacterial networks showed reduced stability despite increased diversity, perhaps linked to the downregulation of ATP-binding cassette (ABC) transporters. Notably, Fe-Mn oxides counteracted Ca influences through selective nutrient adsorption, creating antagonistic selection pressures. Under calcium stress, both Ca and total P (TP) emerge as key drivers of microbial community restructuring, with fungal networks exhibiting significantly greater stability compared to their bacterial counterparts. This study bridges the knowledge gap in the driving mechanisms of microbial communities under soil Ca stress and provides a theoretical basis for improving vegetable yields, with implications for soil management in Ca-rich ecosystems. Full article

Karst rivers are increasingly contaminated by both heavy metals and nanoplastics, yet their combined impact on riparian litter decomposition remains unresolved. We conducted a 90-day microcosm experiment using Miscanthus floridulus leaf litter collected from the Donghe River, Jishou, China, and exposed it to Pb (1 mg L⁻¹), polystyrene nanoplastics (10 and 100 µg L⁻¹), and their combinations. Pb alone modestly inhibited mass loss (61.0%) and respiration, while NP10 significantly accelerated decomposition (67.0%), and NP100 suppressed it (60.4%); co-exposure produced non-monotonic, concentration-dependent effects. Enzyme stoichiometry revealed that all treatments intensified nitrogen limitation but alleviated carbon limitation through reduced microbial activity. Bacterial communities, dominated by Pseudomonadota, exhibited remarkably stable phylum-level composition, high network complexity, and identical keystone taxa across all treatments, indicating strong functional redundancy and resilience. In contrast, fungal communities suffered severe declines in Basidiomycota abundance, collapsed network stability, and a single keystone taxon, underscoring their vulnerability. βNTI–RC_bray analyses demonstrated that stochastic processes (>50%) overwhelmingly governed both bacterial and fungal assembly, with only marginal deterministic shifts. Collectively, our findings highlight that bacteria—not fungi—serve as the primary decomposers under Pb–NP co-stress and that stochastic assembly, coupled with bacterial redundancy, buffers ecosystem function against emerging mixed pollutants in subtropical riverine systems. Full article

Biodegradable mulching films are promoted as alternatives to traditional polyethylene films, but their environmental impacts remain controversial. This study investigates how biodegradable films affect microplastic pollution of soil, fungal community structure, and ecological network stability. We conducted a maize field experiment comparing conventional polyethylene (CF, PE) and biodegradable (BF, PLA + PBAT) film residues. We used scanning electron microscopy and high-throughput sequencing of fungal ITS genes. We assessed soil properties, microplastic release, fungal communities, and network stability through co-occurrence analysis. BF degraded rapidly, releasing microplastic concentrations much higher than CF. BF increased soil carbon and nitrogen and substantially enhanced maize biomass. However, it significantly reduced soil pH and decreased key functional fungi (saprotrophs and symbionts) abundance. The fungal ecological network complexity and stability declined significantly. Correlation analysis revealed positive associations between saprotrophic and symbiotic fungi abundance and network stability. In contrast, CF reduced some nutrient levels but improved fungal network complexity and stability. This study reveals that biodegradable films create an “ecological trap.” Short-term nutrient benefits mask systematic damage to soil microbial network stability. Our findings challenge the notion that “biodegradable equals environmentally friendly.” Environmental assessments of agricultural materials must extend beyond degradability to include microplastic release, functional microbial responses, and ecological network stability. Full article

An experiment was conducted to evaluate the effects of mixed lactic acid bacteria (LAB) plus fibrolytic enzymes (xylanase + β-glucanase) on bacterial and fungal communities in terminal and aerobically exposed whole-plant corn silage ensiled in a temperate zone. Short-season corn forage was either uninoculated (C) or inoculated (I) with a mixture of LAB containing 1.5 × 10⁵ colony-forming units (cfu)/g Lentilactobacillus hilgardii, 1.5 × 10⁵ cfu/g of Lentilactobacillus buchneri, and 1.0 × 10⁵ cfu/g Pediococcus pentosaceus plus a combination of xylanase + β-glucanase. Silage samples were taken after ensiling in bag silos for 418 days (terminal silage; TS), with subsamples of TS subsequently exposed to air for 14 days (aerobically exposed silage; AS). Regardless of treatment, Firmicutes, Proteobacteria, Cyanobacteria, and Actinobacteria were the predominant phyla in the bacterial microbiome, whilst Ascomycota and Basidiomycota were the predominant phyla in the fungal microbiome in both TS and AS. Lactobacillus, Acetobacter, and Bacillus were the most abundant bacterial genera, whilst Candida, Aspergillus, Vishniacozyma, Pichia, and Issatchenkia were the most abundant fungal genera. Use of silage additive did not change bacterial or fungal alpha or beta diversity during ensiling or aerobic exposure, but decreased (p < 0.01) the relative abundance (RA) of Proteobacteria in both TS and AS, increased (p < 0.01) RA of Firmicutes in AS, but did not affect the RA of fungal phyla in either TS or AS. At the genus level, the additive significantly decreased (p < 0.01) RA of Acetobacter in both TS and AS. The silage additive used in this study significantly affected the composition of multiple microbial genera during ensiling and aerobic exposure by shifting bacterial communities towards enhanced aerobic stability. Full article

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased Morchella crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management. Full article

Prescribed burning significantly influences the microbial communities and physicochemical characteristics of forest soils. However, studies on the impacts of prescribed burning on the stability of soil microbial co-occurrence networks, as well as on the combined effects of post-fire soil depth gradients and their interactions on soil physicochemical properties and microbial communities, remain poorly understood. This study was conducted in a subtropical Pinus yunnanensis plantation that has undergone annual prescribed burns since 2007. Using 16S and ITS rRNA gene sequencing techniques alongside analyses of soil physicochemical properties, we collected and examined soil samples from different depths (0–5 cm, 5–10 cm, and 10–20 cm) in June 2024. The study found that prescribed burning enhanced the complexity and stability of bacterial co-occurrence networks, boosting both the diversity (prescribed burning/unburned control: 3/1) and the abundance (prescribed burning/unburned control: 8/2) of key taxa, which were essential for maintaining bacterial community network stability. However, it also intensified competitive interactions (prescribed burning/unburned control: 0.3162/0.0262) within the community. Moreover, prescribed burning had a significant effect on the diversity, structure, and composition of microbial communities and the physicochemical properties in the 0–5 cm soil layer, while also showing notable effects in the 5–20 cm layer. Prescribed burning also enhanced the coupling between the soil environment and bacterial community composition. The bacterial community showed negative correlations with most physicochemical properties. Soil organic matter (SOM) (p = 0.002) and available potassium (AK) (p = 0.042) were identified as key determinants shaping the post-fire bacterial community structure. The relationship between physicochemical parameters and fungal community composition was weaker. Urease (UE) (p = 0.036) and total potassium (TK) (p = 0.001) emerged as two key factors influencing the composition of post-fire fungal communities. These results elucidate the distinct functional roles of bacteria and fungi in post-fire ecosystem recovery, emphasizing their contributions to maintaining the stability and functionality of microbial communities. The study provides valuable insights for refining prescribed burning management strategies to promote sustainable forest ecosystem recovery. Full article

Silvicultural practices significantly influence the diversity and composition of soil fungal communities, which play crucial roles in maintaining forest ecosystem functionality. This study evaluated the impact of three silvicultural treatments, consisting of liberation cutting, first thinning, and second thinning, on rhizospheric fungal and ectomycorrhizal (ECM) fungi communities in Pinus forests located in Puebla, Mexico. Using high-throughput metabarcoding of the internal transcribed spacer (ITS2) region, we identified 346 fungal genera across all treatments, with Ascomycota and Basidiomycota being the dominant phyla. Alpha diversity indices revealed a trend toward higher fungal richness for first thinning, followed by liberation cutting and lower values for second thinning. A beta diversity analysis demonstrated significant shifts in the fungal community composition across treatments, highlighting the influence of the thinning intensity. The proportions of different functional guilds were consistent across the treatments. However, compositional differences were observed, mainly in soil and wood saprotrophs and in pathogenic taxa. Liberation cutting showed enrichment in ECM taxa such as Russula and Cenococcum, whereas Tuber, Humaria, and Tricholoma were decreased for first thinning and Russula was decreased for second thinning. These findings underscore the need for sustainable forest management practices that balance productivity with the conservation of fungal biodiversity to ensure ecosystem stability and functionality. Full article

The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities respond to combined water and nitrogen-phosphorus nutrient changes in karst shrubland remains poorly understood. This knowledge gap hinders effective restoration strategies in karst shrublands. Here, the effects of water, nitrogen, and phosphorous additions and their interactions on soil physico-chemical properties, soil microbial abundance, diversity, community composition, and the co-occurrence network were explored. A full factorial experiment (water × nitrogen × phosphorous, each at two levels) was conducted in a karst shrubland with over 20 years of vegetation restoration, with treatments including control, water (+120 mm yr⁻¹), nitrogen (+20 g N m⁻² yr⁻¹), phosphorus (+16 g P m⁻² yr⁻¹), and their four combinations. Our results suggested that water addition significantly increased soil water content and soil microbial abundance but reduced fungal diversity. Nitrogen addition significantly increased soil nitrate nitrogen content and fungal diversity, and fungal diversity showed an increasing trend under phosphorous addition. The addition of nitrogen and phosphorous did not significantly alter the soil microbial community composition, while water addition showed a tendency to change the soil fungal community composition. Network topological properties, robustness, and vulnerability analyses indicated that individual nitrogen or phosphorous additions, as well as their interactions, reduced network complexity and stability. In contrast, water addition alone or in combination with nitrogen and/or phosphorous alleviated these negative effects, and the water and phosphorous interaction exhibited the highest levels of network complexity and stability. Further analysis showed that the soil pH, available phosphorous, ratio of carbon to phosphorous, and ammonium nitrogen were explanatory variables contributing significantly to soil microbial abundance, diversity, community composition, and network complexity. Overall, these findings highlighted the pivotal role of water availability in enhancing soil microbial stability under nutrient enrichment, offering valuable insights into ecological restoration in karst ecosystems. Full article

The ecological interface between grasslands and farmlands forms a critical landscape component, significantly contributing to the stability and functioning of ecosystems within the agro-pastoral transition zone of northern China. Nevertheless, the variation patterns and interactions between soil physicochemical attributes and microbial community diversity at this interface remain poorly understood. In this study, we investigated nine sites located within 50 m of the grassland–farmland boundary in the Songnen Plain, northeastern China. We assessed the soil’s physicochemical properties and the composition of bacterial and fungal communities across these sites. Results indicated a declining gradient in soil physicochemical characteristics from grassland to farmland, except for pH and total phosphorus (TP). The composition of bacterial and fungal communities differed notably in response to contrasting land-use types across the ecological interface. Soil environmental variables were closely aligned with shifts observed in bacterial and fungal assemblages. Concentrations of total nitrogen (TN), available phosphorus (AP), alkali-hydrolyzable nitrogen (AN), and available potassium (AK) exhibited inverse correlations with both bacterial and fungal populations. Alterations in microbial community composition were significantly linked to TN, TP, total potassium (TK), AN, AP, AK, and soil pH levels. Variability in soil properties, as well as microbial biomass and diversity, was evident across the grassland–cropland boundary. Long-term utilization and conversion of grassland into cultivated land altered the soil’s physicochemical environment, thereby indirectly shaping the structure of microbial communities, including both bacteria and fungi. These findings provide a valuable basis for understanding the ecological implications of land-use transitions and inform microbial-based indicators for assessing soil health in agro-pastoral ecotones. Full article

Coffee pulp, the primary residue generated during the wet processing of Coffea arabica L., is frequently applied directly to fields as a crude soil amendment. However, this practice often lacks proper microbial stabilization, limiting its agronomic potential and posing risks due to the presence of phytotoxic compounds. In Colombia, disease-resistant varieties such as Coffea arabica L. var. Castillo and var. Cenicafé 1, developed by the National Coffee Research Center (Cenicafé), are the amongst the most widely cultivated varieties in the country; however, despite their widespread adoption, the microbial ecology of postharvest residues from these varieties remains poorly characterized. This study aimed to isolate and functionally characterize native microbial communities from the pulp of Coffea arabica var. Castillo and var. Cenicafé 1, and to evaluate their role in postharvest processing and organic waste management. Fresh pulp samples were collected from a wet-processing facility located in tropical mid-elevation zones. A total of 53 microbial isolates were recovered using culture-dependent techniques on selective media targeting yeasts, lactic acid bacteria (LAB), and filamentous fungi. Amplicon sequencing of the 16S rRNA gene (V3–V4 region) and ITS1 region was conducted to profile bacterial and fungal communities, revealing diverse microbial consortia dominated by Aspergillus, Lactobacillus, Leuconostoc, Pichia, and Saccharomyces species. Enzymatic screening indicated high pectinolytic and cellulolytic activity. Composting trials using inoculated pulp showed a ~40% reduction in composting time and improved nutrient content. These findings support the use of native microbiota to enhance composting efficiency and postharvest valorization, contributing to more sustainable and circular coffee systems. Full article