Fungal Diversity Research Articles

Environmental concentrations of the fungicide tebuconazole alter microbial biodiversity and trigger biofilm-released transformation products

Freshwater microbial communities are integral components of riverine biodiversity. The ecological effects of toxic chemical pollutants, such as fungicides (e.g., tebuconazole), on microbial abundance and diversity are needed for risk assessment and regulation. The emergence of RNA metabarcoding approaches allow us to describe at unprecedented resolution the microbial diversity of the active part of a microbial community. Our study assesses the ecotoxicological impact of chronic and acute tebuconazole exposures on fungal, bacterial, and algal biomass and biodiversity of aquatic fungi and bacteria in stream biofilms using an RNA metabarcoding approach. In addition, the study uses HPLC-MS to evaluate the capability of biofilms to metabolize tebuconazole. Natural biofilm communities from a Swedish stream were exposed chronically (24 days) and acutely (96 h) to environmental concentrations of tebuconazole (10 and 100 μg/L) in microcosms conditions. The diversity and community structure of fungi and bacteria was assessed by ITS2 and 16S cDNA amplicon-sequencing, respectively. Biofilms chronically exposed to tebuconazole produced and released unidentified transformation products into the water column, suggesting a biotransformation capability following 24 days of uninterrupted exposure. The fungal biomass markedly decreased by a biomass loss of 40% when chronically exposed to 10 μg/L, and 60% when chronically exposed to 100 μg/L. Bacterial and algal biomass remained comparable with the controls in all tebuconazole treatments. Fungal and bacterial alpha diversity metrics were not significantly impacted, although a decreasing trend in fungal richness was observed with the treatments. However, beta diversity was significantly impacted in both fungal and bacterial compartments. Chronic exposures resulted in a shift in community composition, where taxa potentially more tolerant to tebuconazole (i.e. Lecanoromycetes) replaced more sensitive taxa (i.e. Malasseziomycetes). This study indicates that tebuconazole at environmental concentrations might pose a risk to freshwater systems, mainly due to its high toxicity to fungi.

Unexplored fungal diversity on healthy and dandruff skin.

Unexplored fungal diversity on healthy and dandruff skin.

Craspedodidymum hunanense sp. nov. (Chaetosphaeriaceae, Chaetosphaeriales) and a new record of Aquadictyospora clematidis (Dictyosporiaceae, Pleosporales), from Hunan Province, China

Several freshwater hyphomycetous taxa were collected during a survey of freshwater fungal diversity in Hunan Province, China. Among these new collections, Craspedodidymum hunanense is introduced as a new species, distinguished from other Craspedodidymum species by its large and distinctive funnel-shaped terminal collarette and supported by ITS, LSU, and TEF1-α phylogenetic analyses. Additionally, Aquadictyospora clematidis is reported as a new geographical record in China, with a detailed morphological description and multigene phylogeny based on ITS, LSU, SSU, and TEF1-α. These findings significantly enrich our comprehension of fungal biodiversity in Hunan Province and offer valuable molecular insights.

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing

Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.

Study on the nutritional relationships in mycelia and fruiting bodies of Hypsizygus marmoreus under defined nutrient conditions

Edible fungal fruiting bodies develop from mycelia that experienced physiological knotting, establishing a tight nutrient connection between mycelia and fruiting bodies. Despite this connection, limited research has explored this field. This study aimed to elucidate the crude polysaccharide and protein contents in mycelia and fruiting bodies of 5 main edible fungi cultivars: Flammulina velutipes, Hypsizygus marmoreus, Lyophyllum decastes etc., under defined nutrient conditions. H. marmoreus was selected as an example, the study investigated nutrient relationships in both mycelia and fruiting bodies across 5 media with varying carbon to nitrogen ratios (C/N). Results indicated higher crude polysaccharide and protein contents in mycelia compared to fruiting bodies. A predictive model for the crude polysaccharide and protein contents of H. marmoreus fruiting bodies was developed using partial least squares (PLS) method. Predicted values closely matched experimental determinations, providing the model's accuracy. The impact of different C/N on crude fiber content in the culture media was minimal. Metabolomics analysis of H. marmoreus revealed significant up-regulation of carbohydrate metabolites (72 %) and amino acid metabolites (84 %) in mycelia relative to fruiting bodies. Specifically, metabolites involved in polysaccharide precursor synthesis pathways (Gal1P, Glc-1P, UDP-Glc) and protein precursor synthesis pathways (9 amino acids) showed heightened levels in mycelia, which suggested a possible reason for the observed higher crude polysaccharide and protein content in mycelia compared to fruiting bodies. Overall, these results provide a crucial theoretical foundation for predicting and enhancing edible fungal quality and diversity through mycelial studies. They also establish a cornerstone for accelerating new variety development and optimizing high-quality mushroom production formulations.

A heart-rot fungus, Inonotus obliquus (chaga), mediates microhabitat creation in birch snags and contributes to forest fungal diversity

Ecological significance of fungi in terrestrial ecosystems is generally acknowledged but the ecological networks mediated by particular fungal species are seldom described. In this note, we draw attention to an undescribed function of a well-known heart-rot fungus, Inonotus obliquus (chaga). This species mostly inhabits live birches (Betula), where it forms sterile conks used in ethnomedicine. Less known is that its short-lived fruit-bodies develop under the bark after the tree death and release the spores by cracking the bark. Based on studies in Estonia, we report that this process is a major mechanism that removes bark from standing dead birches and that the exposed wood becomes a distinct woody substrate. We report nearly 50 species of epixylic lichens and allied fungi on birch snags, most notably calicioid fungi, which include several species of conservation concern. Because forest management suppresses that stage through multiple mechanisms (removal of trees with conks and dead trees; shortened rotations; preference for conifer monocultures), the keystone function can be lost even if I. obliquus persists in the area. Additionally, multi-functional forestry that supports chaga for its conk use should pay attention on that later phase of fruit-body formation to maintain natural functioning of this species. Such microhabitat providing functions may be more widespread among fungi that currently acknowledged.

Impact of prescribed fire on fungal communities in Scots pine (Pinus sylvestris) forests in Mediterranean transitional zones

The Mediterranean region is renowned for its natural susceptibility to wildfires. In recent years, this risk has intensified due to various factors, including climate change and rural abandonment. Castilla y Leon stands out as one of the most severely impacted areas grappling with rural exodus. This evolving scenario accentuates the urgency of implementing forest management strategies to mitigate the escalating threat of wildfires, with a primary focus on fuel reduction. Although prescribed fires represent an efficient and cost-effective tool for wildfire prevention, they remain a contentious subject in Europe. Fungi not only contribute significantly to rural economies but also play a pivotal role in maintaining the equilibrium of forest ecosystems. The main objective of this study was to examine the effects of prescribed burning on Pinus sylvestris soils, with a specific focus on the recovery of fungal populations after such fires. To assess the short-term effects of prescribed fires on soil fungal communities, we collected soil samples from both burned and unburned plots 12 months post-burning to perform genomic DNA analyses. Our findings indicate that prescribed burning does not significantly alter fungal diversity or composition, with only litter saprotrophs showing significantly higher levels of abundance in burned areas than in unburned areas. Valuable edible fungi persisted post-burning, suggesting that prescribed burning could be used to reduce wildfire fuel loads while preserving fungal biodiversity and valuable edible fungi. These results advocate for the use of prescribed burning as a viable, myco-friendly forest management practice, offering a balance between fire prevention and ecological conservation.

Plant litter crust enhances nitrogen accumulation by regulating microbial diversity and urease activity in semi-arid sandy soils

Plant litter plays a crucial role in regulating soil nitrogen (N) cycling in dryland ecosystems. However, the mechanisms by which plant litter crust drives microbial community composition to influence N levels in sandy soils remain unclear. In this study, we examined the effects of litter crust on sandy soil microhabitat characteristics (temperature, moisture, and porosity), microbial diversity and composition, urease activity, and soil N variables (total-N, nitrate-N, and ammonium-N) across different stages of litter crust development (including early-, mid-, and post-term) in a field setting. We found that litter crust promotes bacterial and fungal alpha diversity in sandy soils, leading to a shift in bacterial community composition from oligotrophs (i.e., Actinobacteria) to copiotrophs (i.e., Proteobacteria and Bacteroidetes), and a shift in fungal community composition dominance from Ascomycota to Basidiomycota. Litter crust enhances the complexity and stability of bacterial and fungal co-occurrence networks in sandy soils, especially in early- and mid-term stages of crust development. Additionally, litter crust increases nitrification (aerobic ammonia oxidation) and decreases denitrification (nitrate reduction) in these soils. Notably, the increase in soil moisture and urease activity, along with the decrease in soil temperature due to litter crust, effectively promotes N accumulation in sandy soils. Our results demonstrate that N levels during the litter crust period are mainly influenced by a combination of bacterial beta diversity and fungal alpha diversity at the 0–5 cm depth, and bacterial alpha diversity along with soil properties (i.e., soil variables and urease activity) at the 5–10 cm depth. Overall, our results reveal that litter crust contributes to N accumulation in sandy soils by regulating bacterial and fungal community composition and diversity, as well as by buffering soil temperature and soil moisture, and enhancing urease activity. These findings provide new insights into the critical role of soil microbes in maintaining N functions during litter crust development in semi-arid sandy ecosystems.

Grassland irrigation and grazing prohibition have significantly affected vegetation and microbial diversity by changing soil temperature and moisture, evidences from a 6 years experiment of typical temperate grassland

Grasslands are characterized by high primary productivity and offer a diverse array of ecosystem services that contribute to human well-being. The dynamic balance between vegetation-soil in grassland ecosystems is being affected by anthropogenic activities and climate change, in which soil microbial communities play a critical regulating role. However, how microbial biodiversity interacts with vegetation-soil and responds to environmental change remains unclear. We conducted a six-year field experiment in the grasslands of Inner Mongolia to study the effects of grazing and altered precipitation on major vegetation types (or species), soil properties, and microbial community composition. The results showed that increased precipitation influenced positive associations within microbial communities, which helped to increase vegetation diversity. The biomass of Stipa.sareptana increased by 0.054 % under reduced precipitation, while it significantly increased by 2.07 % under the combination of grazing ban and reduced precipitation. Grazing prohibition had a significant negative effect on bacterial diversity and Shannon's index, but a significant positive effect on fungal diversity and abundance. Increasing precipitation had no significant effect on bacterial diversity under grazing conditions, while decreasing precipitation significantly reduced the Shannon index of bacteria. Fungal communities were very sensitive to changes in precipitation, and both increasing and decreasing precipitation significantly affected the structure of fungal communities. In summary, our results highlight how grassland irrigation and moderate grazing can be employed as a management strategy to promote plant diversity and thereby improve ecosystem functioning and resilience.

Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon.

This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.

Gut microbiota and mycobiota change with feeding duration in mice on a high-fat and high-fructose diet

BackgroundMetabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is becoming the most common chronic liver disease. The gut microbiome is regarded to play a crucial role in MAFLD, but the specific changes of gut microbiome, especially fungi, in different stages of MAFLD are not well understood. This study aimed to observe the longitudinal changes of colon bacteria and fungi of mice at different feeding duration of a high-fat and high-fructose diet (HFHFD), and explore the association between the changes and the progression of MAFLD.MethodsTwenty-eight male C57BL6J mice were randomly assigned to the normal diet (ND) group and HFHFD group. At the 8th and 16th weeks, mice were sacrificed to compare the diversity, composition, and co-abundance network of bacteria and fungi in colon contents among groups.ResultsHFHFD-8W mice exhibited increases in Candida and Dorea, and decreases in Oscillospira and Prevotella in comparison to ND-8W mice, HFHFD-16W mice had increases in Bacteroides, Candida, Desulfovibrio, Dorea, Lactobacillus, and Rhodotorula, and decreases in Akkermansia, Aspergillus, Sterigmatomyces, and Vishniacozyma in comparison to ND-16W mice. And compared to HFHFD-8W mice, HFHFD-16W mice had increases in Desulfovibrio, Lactobacillus, Penicillium, and Rhodotorula, and decreases in Talaromyces and Wallemia. Spearman and GEE correlation analysis revealed that Bacteroides, Candida, Desulfovibrio, and Lactobacillus positively correlated with NAFLD activity score (NAS).ConclusionGut microbiota and mycobiota undergo diverse changes at different stages of MAFLD.Clinical trial numberNot applicable.

Nitrogen deposition changes the root nutrient uptake strategies by affecting microbial diversity of the rhizosphere

Despite the acknowledged importance of rhizosphere fungi in ecosystem functioning, their role in mediating the effects of environmental changes on plant root nutrient uptake strategies remains inadequately understood. To address this gap, long-term nitrogen addition field experiments were conducted to investigate how rhizosphere fungal diversity influences specific root length, a pivotal indicator of plant nutrient uptake rate. The results of the study showed that nitrogen addition significantly augmented specific root length and rhizosphere fungal diversity in both arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree species. However, the effects on rhizosphere fungal diversity differed markedly between the two mycorrhizal types. In AM tree species, nitrogen addition decreased rhizosphere beneficial fungal diversity while increasing the diversity of pathogenic fungi. Conversely, ECM tree species exhibited an increase in rhizosphere beneficial fungal diversity and a reduction in pathogenic fungal diversity under nitrogen addition. Furthermore, we identified a positive correlation between the diversity of rhizosphere pathogens and specific root length under nitrogen addition, while a negative correlation was observed under the control. Structural equation modeling further revealed that the indirect effects of nitrogen addition on SRL were mediated through changes in the diversity of rhizosphere beneficial fungi. These findings suggest that nitrogen addition not only directly influences SRL but also exerts significant indirect effects by altering the microbial composition of the rhizosphere. In summary, the study underscores the substantial impact of long-term nitrogen addition on the interactive mechanism of plant physiological characteristics, mediated by pathogenic and beneficial fungi in the rhizosphere of temperate forests.

Bacterial and fungal diversity, community composition, functional groups, and co-occurrence network succession in dryland and paddy soils along a 3000-year chronosequence

There is a limited understanding of soil microbial community successional trajectories during dryland and paddy soil long-term management after wetland reclamation. We examined the effects of long-term reclamation on the microbial diversity, community composition, functional groups, and co-occurrence network in dryland and paddy soils using a 3000-year soil chronosequence established in the floodplain of the middle and lower Yangtze River, employing the “space-for-time” method and 16S rRNA and ITS amplicon sequencing. Over time, reclaimed land experienced varying losses in microbial richness and diversity, with paddy soils exhibiting higher alpha diversity than drylands due to greater resources and ecological niches. Proteobacteria dominated drylands, Chloroflexi prevailed in paddy soils, and fungal communities in both land-use types were primarily Ascomycota and Basidiomycota. Functional predictions showed higher chemoheterotrophy and aerobic_chemoheterotrophy in dryland soils and more animal_parasites_or_symbionts and dung_saprotrophs in paddy soils. During the 2000–3000 year reclamation, the abundance of pathogens increased, posing risks to agricultural production. Co-occurrence network analysis indicated that, compared to paddy soils, dryland soils may form a more complex and stable microbial cooperative network. Soil organic carbon and pH influenced microbial communities in drylands, while bulk density and cation exchange capacity were crucial in paddy soils. Partial least squares path modeling indicated that reclamation duration impacts microbial network complexity and diversity, with soil properties regulating paddy soil microbial networks. These findings broaden our understanding of microbial community succession in dryland and paddy soils after long-term wetland reclamation, supporting soil health and sustainable agriculture.

How do attached crown parts and branches contribute to the diversity of saproxylic fungi and beetles in downed and decaying spruce trees?

AbstractA significant proportion of forest-dwelling species in boreal forests are saproxylic, i.e., dependent on deadwood. To safeguard deadwood-associated diversity in managed forest landscapes, it is important to understand how substrate preferences and specialization structure saproxylic species communities across different deadwood resource types. In this study, we investigated the diversity and associations of saproxylic fungi and beetles at the scale of entire trees to understand how different tree parts contribute to species diversity. To do this, we sampled species assemblages in trunks (d > 15 cm), tops (d 5–10 cm) and branches (d < 5 cm) of 31 fallen Norway spruce trees. Fungal assemblages were investigated with DNA metabarcoding from wood samples, and beetles were surveyed by bark peeling and sieving. Our results showed that, fungal and beetle assemblages were clearly differentiated between trunks and branches. In the tops, fungal community composition was intermediate between trunks and branches, whereas beetle species composition was more closely aligned with trunks. Trunks and branches both harbored specialized fungal and beetle species, but no species were identified as specialists of tops. Fungal and beetle richness were lowest in branches, and fungal richness peaked in tops. Substrate specialization of saproxylic species at the scale of individual trees imply that deadwood restoration in managed forests should prioritize whole-tree retention instead of partial retention such as artificial high stumps or pruned logs.

Effects of stand age and soil microbial communities on soil respiration throughout the growth cycle of poplar plantations in northeastern China

IntroductionMany studies have identified stand age and soil microbial communities as key factors influencing soil respiration (Rs). However, the effects of stand age on Rs and soil microbial communities throughout the growth cycle of poplar (Populus euramevicana cv.‘I-214’) plantations remain unclear.MethodsIn this study, we adopted a spatial approach instead of a temporal one to investigate Rs and soil microbial communities in poplar plantations of 15 different ages (1–15 years old).ResultsThe results showed that Rs exhibited clear seasonal dynamics, with the highest rates observed in the first year of stand age (1-year-old). As stand age increased, Rs showed a significant decreasing trend. We further identified r-selected microbial communities (copiotrophic species) as key biological factors influencing the decline in Rs with increasing stand age. Other abiotic factors, such as soil temperature (ST), pH, soil organic carbon (SOC), nitrate nitrogen (NO3−-N), and the C/N ratio of plant litter (Litter C/N), were also significantly correlated with Rs. Increased stand age promoted fungal community diversity but suppressed bacterial community diversity. Bacterial and fungal communities differed significantly in abundance, composition, and function, with the Litter C/N ratio being a key variable affected by microbial community changes.ConclusionThis study provides crucial empirical evidence on how stand age affects Rs, highlighting the connection between microbial community assemblages, their trophic strategies, and Rs over the growth cycle of poplar plantations.

Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment–Water Interface in a Subalpine Lake

The sediment–water interface is the most active region for biogeochemical processes and biological communities in aquatic ecosystems. As the main drivers of biogeochemical cycles, the assembly mechanisms and the distribution characteristics of microbial communities at this boundary remain unclear. This study investigated the microbial communities across the sediment–water interface in a natural subalpine lake in China. The results indicated that the diversity of bacterial communities in middle sediment was significantly higher than that in overlying water and other sediments (p < 0.001). Pearson’s correlation analysis indicated that the diversity was significantly influenced by biotic factors (e.g., diversity of fungus, protozoan and alga) and physicochemical parameters (e.g., total carbon, total organic carbon, nitrate, ammonium and pH) (p < 0.01). Null model analysis revealed that the homogeneous selection dominated the assembly of the bacteria community in sediment, whereas the heterogeneous selection dominated that in overlying water. The least squares path analysis showed that interactions between protozoa and bacteria had a greater impact on bacterial community assembly (p < 0.001). Important taxa influence the assembly by regulating biotic interactions. These findings provided a basis for understanding the importance of biotic interactions in maintaining subalpine lakes’ ecosystems across the sediment–water interface.

Soil respiration related to the molecular composition of soil organic matter in subtropical and temperate forests under soil warming

The chemical composition and degradability of soil organic matter (SOM) are among the most important factors influencing the feedback between soil CO2 emissions and climate warming. We hypothesized that the response of soil respiration to long-term warming in various forest ecosystems depends on how soil warming alters the chemical composition of SOM. Therefore, we compared the effects of long-term soil warming on soil respiration, SOM molecular structure, and bacterial and fungal diversity in two forest ecosystems in the southern subtropical and warm temperate zones of China. In the subtropical forest, soil warming did not affect soil respiration in the short term (2–3 years) but decreased it in the longer term (10 years, −10%). The decline in soil respiration was associated with an increased aliphaticity of SOM and lower O-alkyl C content, along with an increased abundance of microbial K-strategists over time. In the warm temperate forest, soil warming significantly stimulated soil respiration by 35% in the short term and 30% in the long term. The sustained positive response to warming was likely related to the increased decomposability of SOM owing to increased root C input. Our results suggest that the molecular composition of SOM is affected by warming and in turn feeds back to longer-term soil respiration responses. The different responses at the two study sites suggest considerable variation in the feedback within different forest ecosystems.

Impact of bacterial inoculations on Pisum sativum L. biometric parameters and associated bacterial and AM fungal communities under semi-arid field conditions in Tunisia

In Mediterranean agroecosystems, pea (Pisum sativum L.) is one important crop due to its nutritional benefits and high protein content. However, soil nutrient availability and soil health are known to affect pea productivity, especially under arid and semi-arid conditions. Currently, the use of plant growth-promoting bacteria (PGPB) may represent a bio-based tool to improve pea productivity in drought-affected areas. Nevertheless, there is limited knowledge on how PGPB inoculations in field could impact native communities of bacteria and arbuscular mycorrhizal fungi (AMF) in these areas. Here, a two-year field study in Tunisia was established to evaluate the effects of inoculating two pea varieties with three strains of potential PGPB, including Rhizobium laguerreae and two strains of Erwinia sp., on agronomic performance and soil microbial communities. Inoculations improved productivity and all measured biometric parameters, with the treatment including a consortia of the three strains showing the highest benefits. Metabarcoding analysis showed an increased bacterial and AM fungal diversity in soil of inoculated plants. Additionally, specific AMF-bacterial associations were identified, suggesting a synergistic role in enhancing soil health and pea growth. Overall, this study highlights the potential of targeted bacterial inoculations to improve pea performance under semi-arid environments by exploiting beneficial plant-microbe interactions. These results support the use of microbial inoculants as a sustainable agricultural practice in semi-arid areas, also improving the understanding of their impact on native bacterial and AM fungal communities.

Rhizosphere Shifts: Reduced Fungal Diversity and Microbial Community Functionality Enhance Plant Adaptation in Continuous Cropping Systems

Continuous cropping problems constitute threats to perennial plant health and survival. Soil conditioners have the potential to enhance plant disease resistance in continuous cropping systems. However, how microbes and metabolites of the rhizosphere respond to soil conditioner addition remains largely unknown, but this knowledge is paramount to providing innovative strategies to enhance plant adaptation in continuous cropping systems. Here, we found that a biochar conditioner significantly improved plant survival rates in a continuous cropping system. The biochar-induced rhizosphere significantly alters the fungal community, causing a decline in fungal diversity and the downregulation of soil microbial community functionality. Specifically, the biochar-induced rhizosphere causes a reduction in the relative abundance of pathogenic Fusarium sp. and phenolic acid concentration, whose variations are the primary causes of continuous cropping problems. Conversely, we observed an unexpected bacterial diversity increase in rhizospheric and non-rhizospheric soils. Our research further identified key microbial taxa in the biochar-induced rhizosphere, namely, Monographella, Acremonium, Geosmithia, and Funneliformis, which enhance soil nutrient availability, suppress Fusarium sp., mitigate soil acidification, and reduce phenolic acid concentrations. Collectively, we highlight the critical role of regular microbial communities and metabolites in determining plant health during continuous cropping and propose a synthetic microbial community framework for further optimizing the ecological functions of the rhizosphere.

Structural Characteristics and Driving Factors of Rhizosphere Microbial Communities in the Rhizosphere of Six Stipa Species Across the Ningxia Steppe

The relation and interaction of rhizosphere microbial communities with local environmental factors and root traits is currently a vibrant research hotspot. Yet little is known about how the morphological and functional properties of roots in steppe plants affect microbial community structure. Hence, this study investigated the rhizosphere soil of six Stipa species across the Ningxia steppe in China to examine how the composition of their microbial communities responds to both root traits as well as surrounding environmental factors. Our results reveal significant differences (p < 0.001) in the composition of rhizosphere microbial communities among different Stipa species. The dominant bacterial and fungal phyla are Proteobacteria and Ascomycota, respectively; further, Mortierellomycota plays a key role in the fungal community and is closely associated with other fungal taxa. According to the functional gene predictions for bacteria and fungi, the rhizosphere microbes associated with Stipa species are mainly related to organic matter metabolism and nitrogen cycling. We find that soil physicochemical properties (SOC, TN, TP, AP, SWC, FL, SL) and root traits (RTD, Rtn) are pivotal factors which directly influence the structure of microbial communities dwelling in the rhizosphere of Stipa species. The dominant phyla of fungi and bacteria can respond to those properties in two contrasting ways. One group, consisting of bacteria such as Acidobacteria and fungi like Mortierellomycota, has a relative abundance that is positively correlated with soil nutrients (SOC, TN, AN, TP), whereas the second group, which includes bacteria such as Bacteroidetes and fungi like Ascomycota, is characterized by a negative correlation. More importantly, our results show that root traits significantly impact (p < 0.001) fungal diversity, whereby the morphological and functional properties indirectly affect the composition of bacterial and fungal communities by modulating soil properties. Altogether, the findings suggest that the morphological and functional properties of Stipa roots play a prominent role in shaping the community structure of rhizosphere microbes in steppe, providing a theoretical basis for exploring changes in these communities across space and time, as well as offering insights for grassland conservation and sustainable management.