Search Results (25)

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

Litter decomposition dynamics are largely governed by microbial interactions. While the involvement of endophytic fungi in early-stage decomposition and microbial succession is well established, their species-specific contributions to decomposer community assembly remain insufficiently understood. This study investigated the effects of single-strain endophytic colonization using dominant species (Tubakia dryina, Tubakia dryinoides, Guignardia sp.) and rare species (Neofusicoccum parvum, Penicillium citrinum) on Quercus acutissima leaf decomposition through a controlled field experiment in a karst ecosystem. Endophytes accelerated decomposition rates across treatments but paradoxically reduced transient CO₂ emissions, linked to intensified microbial carbon and phosphorus limitations in late stages. Contrary to expectations, decomposition efficiency was governed by endophytic fungal species traits rather than colonization abundance, with rare species outperforming dominant taxa. Endophytes induced significant fungal community restructuring, reducing Ascomycota while enriching lignin-degrading Basidiomycota, but minimally affected bacterial composition. Co-occurrence networks revealed endophyte-driven fragmentation of microbial connectivity, with only two keystone fungal hubs (Trechispora sp. and Russula carmesina) identified compared to natural communities. Endophytic colonization improved fungal community assembly, mediated by an increase in lignin-degrading Basidiomycota and the suppression of pathogenic Leotiomycetes lineages. Our findings demonstrate that endophytes hierarchically regulate decomposer communities through phylogenetically conserved fungal interactions, prioritizing functional trait selection over competitive dominance, thereby stabilizing decomposition under nutrient constraints. This mechanistic framework advances predictions of litter decay dynamics in forest ecosystems undergoing microbial community perturbations. Full article

Fairy ring fungi are considered keystone species in grasslands due to their strong impact on soil physicochemical properties, but their effect on the associated bacterial community is poorly understood. Here, we analyze shifts in soil bacterial diversity and community composition across fairy rings using Illumina metabarcoding. A total of 254,135 MiSeq reads and between 405 and 1444 operational taxonomic units (OTUs) per soil sample were observed in a montane grassland in the Eastern Pyrenees. We found a strong reduction in all bacterial diversity indices inside the ring-affected zones compared to the outside grassland, especially in the stimulation (current ring) zone. The exception were Firmicutes, the dominant taxa in the grassland, which increased their relative abundance further in fairy ring-affected zones. The recovery of bacterial populations after the fungal front passage highlights the strong resilience of the bacterial communities to this biotic disturbance. Full article

Oral fungal homeostasis is closely related to the state of human health, and its composition is influenced by various factors. At present, the effects of long-term soil heavy metal exposure on the oral fungi of local populations have not been adequately studied. In this study, we used inductively coupled plasma–mass spectrometry (ICP-MS) to detect heavy metals in agricultural soils from two areas in Gansu Province, northwestern China. ITS amplicon sequencing was used to analyze the community composition of oral buccal mucosa fungi from local village residents. Simultaneously, the functional annotation of fungi was performed using FUNGuild, and co-occurrence networks were constructed to analyze the interactions of different functional fungi. The results showed that the species diversity of the oral fungi of local populations in the soil heavy metal exposure group was lower than that of the control population. The relative abundance of Apiotrichum and Cutaneotrichosporon was higher in the exposure group than in the control group. In addition, Cutaneotrichosporon is an Animal Pathogen, which may lead to an increased probability of disease in the exposure group. Meanwhile, there were significant differences in the co-occurrence network structure between the two groups. The control group had a larger and more stable network than the exposure group. Eight keystone taxa were observed in the network of the control group, while none were observed in that of the exposure group. In conclusion, heavy metal exposure may increase the risk of diseases associated with Apiotrichum and Cutaneotrichosporon infection in the local populations. It can also lead to the loss of keystone taxa and the reduced stability of the oral fungal network. The above results illustrated that heavy metal exposure impairs oral fungal interactions in the population. This study extends our understanding of the biodiversity of oral fungi in the population and provides new insights for further studies on the factors influencing oral fungal homeostasis. Full article

Incorporation of plant residues in soil affects microbial community structure and ecological function, which can improve soil fertility. It is reported that substrate qualities could regulate microbial keystone taxa and their interactions, wielding an important effect on nutrient cycling in ecosystems, such as soil labile phosphorus (P) transformation. However, there is little understanding of the specific microbial mechanisms governing P’s availability in acidic soils following the incorporation of plant residues of various qualities. In this 210-day incubation experiment, two high-quality residues of pumpkin stover and mango branch and one low-quality residue of rice straw, different in terms of their labile carbon (C) content and carbon/phosphorus ratio (C/P), were separately mixed with an acidic soil. The aim was to investigate how the residues affected the community composition, keystone species, and interaction patterns of soil bacteria and fungi, and how these microbial characteristics altered soil P mineralization and immobilization processes, along with P availability. The results showed that adding high-quality pumpkin stover significantly increased the soil’s available P content (AP), microbial biomass P content (MBP), and acid phosphatase activity (ACP), by 63.7%, 86.7%, and 171.7% compared to the control with no plant residue addition, respectively. This was explained by both the high abundance of dominant bacteria (Kribbella) and the positive interactions among fungal keystone species. Adding mango branch and rice straw induced cooperation within fungal communities while resulting in lower bacterial abundances, thereby increasing AP, MBP, and ACP less than the addition of pumpkin stover. Moreover, the labile C of plant residues played a dominant role in soil P transformation and determined the P availability of the acidic soil. Therefore, it may be suitable to incorporate high-quality plant residues with high labile C and low C/P into acidic soils in order to improve microbial communities and enhance P availability. Full article

Intercropping affects soil microbial community structure significantly; however, the effects on understory medicinal plants in karst areas remain unclear. We investigated the effects of four intercropping systems (Moso bamboo, Chinese fir, bamboo-fir mixed forest, and forest gap) on the rhizosphere microbial communities of giant lily (Cardiocrinum giganteum), an economically important medicinal plant in China. We assessed the intercropping impact on rhizosphere microbial diversity, composition, and co-occurrence networks and identified key soil properties driving the changes. Bacterial and fungal diversity were assessed by 16S rRNA and ITS gene sequencing, respectively; soil physicochemical properties and enzyme activities were measured. Moso bamboo system had the highest fungal diversity, with relatively high bacterial diversity. It promoted a distinct microbial community structure with significant Actinobacteria and saprotrophic fungi enrichment. Soil organic carbon, total nitrogen, and available potassium were the most influential drivers of microbial community structure. Co-occurrence network analysis revealed that the microbial network in the Moso bamboo system was the most complex and highly interconnected, with a higher proportion of positive interactions and a greater number of keystone taxa. Thus, integrating Moso bamboo into intercropping systems can enhance soil fertility, microbial diversity, and ecological interactions in the giant lily rhizosphere in karst forests. Full article

(1) Background: Plant diversity has long been assumed to predict soil microbial diversity. The mutualistic symbiosis between forest trees and ectomycorrhizal (EM) fungi favors strong correlations of EM fungal diversity with host density in terrestrial ecosystems. Nevertheless, in contrast with host tree effects, neighboring plant effects are less well studied. (2) Methods: In the study presented herein, we examined the α-diversity, community composition, and co-occurrence patterns of EM fungi in Quercus acutissima across different forest types (pure forests, mixed forests with Pinus tabuliformis, and mixed forests with other broadleaved species) to ascertain how the EM fungi of focal trees are related to their neighboring plants and to identify the underlying mechanisms that contribute to this relationship. (3) Results: The EM fungal community exhibited an overall modest but positive correlation with neighboring plant richness, with the associations being more pronounced in mixed forests. This neighboring effect was mediated by altered abiotic (i.e., SOC, TN, LC, and LP) and biotic (i.e., bacterial community) factors in rhizosphere soil. Further analysis revealed that Tomentella_badia, Tomentella_galzinii, and Sebacina_incrustans exhibited the most significant correlations with plant and EM fungal diversity. These keystone taxa featured low relative abundance and clear habitat preferences and shared similar physiological traits that promote nutrient uptake through contact, short-distance and medium-distance smooth contact-based exploration types, thereby enhancing the potential correlations between EM fungi and the neighboring plant community. (4) Conclusions: Our findings contribute to the comprehension of the effect of neighboring plants on the EM fungal community of focal trees of different forest communities and the biodiversity sensitivity to environmental change. Full article

Managing carbon input from crop straw in cropland ecosystems could increase soil organic carbon (SOC) sequestration to achieve C neutrality and mitigate climate change. The complexity of the chemical structures of crop residue largely affects SOC sequestration. Fungi communities play an important role in the degradation of crop residues. However, the relationship between the fungal community composition and the chemical structures of crop residues remains unclear and requires further investigation. Therefore, a 120-day incubation experiment was conducted in Mollisols in Northeast China to investigate the decomposition processes and dynamics of maize straw stem (ST), leaf (LE) and sheath (SH) residues using ¹³C-NMR spectroscopy. Additionally, the microbiomes associated with these residues were analyzed through high-throughput sequencing to explore their relationship. Our results showed that the alkyl C contents in all treatments exhibited increases ranging from 15.1% to 49.1%, while the O-alkyl C contents decreased, ranging from 0.02% to 11.2%, with the incubation time. The A/OA ratios of ST, LE and SH treatments were increased by 23.7%, 43.4% and 49.3% with incubation time, respectively. During the early stages of straw decomposition, Ascomycota dominated, and in the later stage, Basidiomycota were predominant. The class of Sordariomycetes played a key role in the chemistry transformation of straw tissues during decomposition. The keystone taxa abundances, Fusarium_kyushuense, and Striatibotrys_eucylindrospora, showed strong negative correlations with di-O-alkyl C and carbonyl-C content and positive correlations with the β-glucosidase and peroxidase enzyme activity, respectively. In conclusion, our study demonstrated that the keystone taxa play a significant role in regulating the chemical structures of straw tissues, providing a better understanding of the influence of residue quality on SOC sequestration. Full article

Green manure (GM)–rice–rice rotation is an important management practice for improving soil fertility and rice productivity. The microbiological mechanisms for the increase in grain yield in GM–rice–rice rotation remain unclear. The responses of soil biodiversity, bacterial and fungal communities, and their interactions in the GM–rice–rice rotation were investigated based on two long-term field experiments in Gaoqiao (GQ) and Nanxian (NX) in Hunan Province, south China. Results showed that rice yields were raised by 11.79% and 15.03% under GM in GQ and NX, respectively. GM promoted Shannon diversity and Pielou’s evenness and changed the community structures of bacteria and fungi. The co-occurrence network analysis found that the percentages of negative edges were higher in GM (40.79% and 44.32% in GQ and NX, respectively) than those in the corresponding winter fallow (34.86% and 29.13% in GQ and NX, respectively) in the combined bacterial–fungal networks, suggesting more stable microbial community under GM. Moreover, GM had higher percentages of bacterial–fungal and fungal–fungal edges than winter fallow, indicating that GM increased the interaction between bacteria and fungi and fungi play more essential roles in affecting soil processes under GM. The keystone taxa in GM were positively linked with C metabolism-related enzymes and soil multifunctionality, and were important in improving soil fertility and rice productivity. We concluded that the fungal community was more sensitive to GM application than the bacterial community and that keystone taxa had important influences on soil properties and rice productivity in the GM–double-rice cropping system, which can effectively support the sustainable development of the paddy field ecosystem in southern China. Full article

The priming effect (PE) is important for understanding the decomposition of soil organic matter (SOM) and forecasting C-climate feedback. However, there are limited studies on microbial community-level properties and the keystone taxa involved in the process. In this study, we collected soil from a subtropical Phyllostachys edulis forest undergoing long-term N-addition and conducted an incubation experiment to evaluate the effects of single and repeated addition of ¹³C-labeled glucose. Our results demonstrated that previously N-fertilized soil had a smaller cumulative PE compared with that of the control (11% average decrease). This could be primarily explained (26%) by the lower abundance of bacterial r-strategy group members (B_mod#2, constituting Proteobacteria, Firmicutes, and Actinobacteria phyla) under N-addition treatments. A single C-addition induced a greater PE than that of repeated C-additions (2.66- to 3.11-fold). Single C addition led to greater C to N ratios of microbial biomass and fungi to bacteria, positively impacting cumulative PE, indicating that the shifts in fungal/bacterial dominance play an important role in regulating PE. Moreover, a saprophytic taxa group (F_Mod#3, primarily composed of the phyla Ascomycota) explained 62% of the differences in cumulative PE between single and repeated C-additions. Compared with repeated C-additions, a greater abundance of B_Mod#2 and F_Mod#3, as well as C-related hydrolase activity, was observed under single C-addition, inducing greater cumulative PE. Therefore, sufficient C may facilitate the proliferation of r-strategy bacterial taxa and saprophytic fungal taxa, thereby increasing SOM decomposition. Our findings provide novel insights into the relationship between microbial community-level properties and PE. Full article

The interaction between invasive plants and soil microbial communities is critical for plant establishment. However, little is known about the assembly and co-occurrence patterns of fungal communities in the rhizosphere soil of Amaranthus palmeri. The soil fungal communities and co-occurrence networks were investigated in 22 invaded patches and 22 native patches using high-throughput Illumina sequencing. Despite having little effect on alpha diversity, plant invasion significantly altered the composition of the soil fungal community (ANOSIM, p < 0.05). Fungal taxa associated with plant invasion were identified using linear discriminant analysis effect size (LEfSe). In the rhizosphere soil of A. palmeri, Basidiomycota was significantly enriched, while Ascomycota and Glomeromycota were significantly reduced when compared to native plants. At the genus level, the invasion of A. palmeri dramatically increased the abundance of beneficial fungi and potential antagonists such as Dioszegia, Tilletiopsis, Colacogloea, and Chaetomium, while it significantly decreased the abundance of pathogenic fungi such as Alternaria and Phaeosphaeria. Plant invasion reduced the average degree and average path length, and increased the modularity value, resulting in a less complex but more effective and stable network. Our findings improved the knowledge of the soil fungal communities, network co-occurrence patterns, and keystone taxa in A. palmeri-invaded ecosystems. Full article

Microorganisms play essential roles in soil-ecosystem multifunctionality. However, the contribution of their community assembly processes, composition, diversity, and keystone species to ecosystem multifunctionality is unclear, especially in tea-plantation ecosystems. In order to assess the effects of various intercropping patterns (tea-plant monoculture and tea plants, respectively, intercropped with soybean, soybean—milk vetch, soybean—red clover, and soybean—smooth vetch) on soil rare and abundant taxa, a field experiment was carried out. We found that tea plantation intercropping with legumes improved the soil-ecosystem multifunctionality by altering the soil environment, and ultimately benefited nutrient absorption and quality improvement of tea leaves. Whether it was in bacteria or fungi, rare taxa had a higher proportion of deterministic processes in community assembly than abundant taxa. Additionally, intercropping practices changed the soil environment, and rare bacterial taxa were assembled and shifted from variable selection to homogeneous dispersal. Intercropping practices significantly changed the bacterial and fungal communities’ composition, and rare taxa had higher α-diversity than abundant taxa. Increasing legume species in intercropping practice enhanced community dissimilarity to the tea monoculture by affecting soil pH, ammonium nitrogen, and nitrate nitrogen. Rare bacterial and fungal β-diversity exhibited stronger positive relationships with ecosystem multifunctionality (both average and multi-threshold approaches) compared to the corresponding abundant taxa. Furthermore, ecosystem multifunctionality under different intercropping practices was closely related to the keystone rare operational taxonomic units, especially rare bacterial species of Chloroflexi. Our results emphasize the disparate feedbacks of rare and abundant taxa to diverse intercropping practices, as well as the important connection between rare bacterial taxa and ecosystem multifunctionality. Full article

Sugar beet production is threatened by beetroot rot, which can be triggered by consecutive monoculture. Previous studies have shown the beneficial function of microbes affiliated with different plant compartments in inhibiting various plant pathogens. However, whether sugar beet root can recruit particular microbes at the risk of beet rot is still unclear. Therefore, this study explored the composition and community structure of bacteria and fungi of the different compartments (endosphere root, rhizosphere, bulk soil) under two farming modes (monoculture and rotation). Our result showed that the farming mode significantly affected the community structure of bacteria and fungi in bulk soil. In the rhizosphere, the community structures of bacteria between the two varieties were similar under rotation mode, and markedly different under monoculture mode. The bacterial and fungal diversity in the rhizosphere and endophytic root of the rot-suppressive variety was higher than in the rot-conducive variety. Under monoculture mode, the beneficial microbes as biomarkers were enriched in the rot-resistant variety, e.g., operational taxonomic units (OTUs) affiliated to the genus of Sordariomycetes, Cordycipitaceae, Lecanicillium, Plectosphaerellaceae, S085, Pedosphaeraceae in the rhizosphere and the genus of Actinobacteria, and Pseudonocardia, Exobasidiomycetes in the endophytic root, while for the rot-conducive variety, OTUs affiliated to the genus of Chitinophagaceae, Flavisolibacter in the rhizosphere and the Novosphingobium, Sphingobacterium, Tilletiopsis_washingtonensis, and Flavobacterium in the endophytic root. The network analysis showed that OTUs affiliated to the order of Saccharimonadales, Anaerolineae, the family of Saprospiraceae, the genus of Subgroup_10 (belonging to the family of Thermoanaerobaculaceae), Lysobacter, and AKYG587 were the keystone taxa in the rot-suppressive variety, while both beneficial and harmful microbes in the rot-conducive variety, such as Pedobacter, Ferruginibacter, and P3OB-42, were present. The variation in soil pH was shown to be the critical contributor to the microbial difference. In summary, the farming mode is critical in shaping bulk soil microbial structure by changing soil pH. Under monoculture mode, the rot-suppressive variety has more microbial diversity in both the rhizosphere and endophytic root, and enriched different beneficial microbes relative to the rot-conducive variety; the underlying mechanisms and associations of critical microbes are worth further investigation. Full article

The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring. Full article

Until recently, a comprehensive evaluation of the environmental drivers on the abundance and structure of the microbial community in typical forest soils has not been thoroughly conducted. In this study, the typical forest soils (Mongolian oak (Quercus mongolica) soil, MOS; white birch (Betula platyphylla) soil, WBS; and white poplar (Populus davidiana) soil, WPS) in the Sanjiang Plain were selected to ascertain the differences and the major environmental factors driving soil microbial community abundance and structure. Results indicated that differences existed in the abundance and structure of the bacterial, archaeal, and fungal community. Co-occurrence network analysis showed that the bacterial and fungal networks were more complex than those of archaeal networks. Unclassified Acidobacteria and unclassified Pyrinomonadaceae were the keystone taxa in the bacterial networks, while Pleotrichocladium and Leotia were the keystone taxa in the fungal networks. Among all environmental factors, pH, SOM, and total N exhibited dominant roles in affecting the abundance of bacteria, archaea, and fungi. The redundancy analysis (RDA) showed that pH was the vital environmental factor responsible for driving the structure of the bacterial, archaeal, and fungal community. Full article