Rhizosphere Fungal Community Structure Research Articles

Effects of Bacillus velezensis GUAL210 control on edible rose black spot disease and soil fungal community structure.

Rose black spot is an economically important disease that significantly decreases flower yield. Fungicide and biological control are effective approaches for controlling rose black spot. The objective of this study was to evaluate the effect of application of biological and chemical control agents, including Bacillus velezensis (GUAL210), Bacillus sp. (LKW) and fungicide (CP) on the black spot disease and rhizosphere fungal community structure of edible rose. In this study, the R. chinensis 'Crimson Glory' was taken as the research object, and the field experiment was designed by randomized block design. The experiment contained 3 treatments (CP, GUAL210, LKW) and 1 control. The control effect and growth promoting effect of fungicide and biological control on rose black spot were compared. The composition and diversity of rhizosphere soil fungal community of different treatments of rose were studied by high-throughput sequencing method. The fungal community composition, correlation of environmental factors and differences in metabolic pathways related to rose disease were analyzed, and the correlation between rhizosphere soil fungal community of rose and biological control of disease was explored. Both disease incidence and disease index differed significantly among groups (LKW < GUAL210 < CP < CK), and disease control effect exhibited no significant difference between GUAL210 and LKW (60.96% and 63.86%, respectively). Biological control was superior to chemical control in terms of disease prevention effects and duration, and it significantly increased the number of branches and flowers of rose plants. Ascomycota and Basidiomycota accounted for more than 74% of the total fungal abundance, and the abundance of Ascomycota was highest in CK, followed by GUAL210, CP and LKW, which was consistent with the disease occurrence in each group. The analysis of metabolic pathways showed that the HSERMETANA-PWY in each experimental group was significantly lower than that in control group. The Shannon index in each experimental group was significantly lower than that in control group. PCoA analysis showed that the rhizosphere fungal community structure in each experimental group was significantly different from that in control group. Trichoderma, Paraphaeosphaeria, Suillus, Umbelopsis in GUAL210, and Galerina in LKW replaced Mortierella, Pestalotiopsis, Ustilaginoidea, Paraconiothyrium, Fusarium, and Alternaria as dominant flora, and played a nonneglectable role in reducing disease occurrence. The difference in rhizosphere fungal community structure had an important impact on the incidence of rose black spot disease. Biological control is crucial for establishing environment-friendly ecological agriculture. GUAL210 has promising prospects for application and development, and may be a good substitute for chemical control agents.

Root exudates influence rhizosphere fungi and thereby synergistically regulate Panax ginseng yield and quality.

Root exudates contain a complex array of primary and specialized metabolites that play important roles in plant growth due to their stimulatory and inhibitory activities that can select for specific microbes. In this study, we investigated the effects of different root exudate concentrations on the growth of ginseng (Panax ginseng C. A. Mey), ginsenoside levels, and soil fungal community composition and diversity. The results showed that low root exudate concentrations in the soil promoted ginseng rhizome biomass and ginsenoside levels (Rg1, Re, Rf, Rg2, Rb1, Ro, Rc, Rb2, Rb3, and Rd) in rhizomes. However, the rhizome biomass and ginsenoside levels gradually decreased with further increases in the root exudate concentration. ITS sequencing showed that low root exudate concentrations in the soil hardly altered the rhizosphere fungal community structure. High root exudate concentrations altered the structure, involving microecological imbalance, with reduced abundances of potentially beneficial fungi (such as Mortierella) and increased abundances of potentially pathogenic fungi (such as Fusarium). Correlation analysis showed that rhizome biomass and ginsenoside levels were significantly positively correlated with the abundances of potentially beneficial fungi, while the opposite was true for potentially pathogenic fungi. Overall, low root exudate concentrations promote the growth and development of ginseng; high root exudate concentrations lead to an imbalance in the rhizosphere fungal community of ginseng and reduce the plant's adaptability. This may be an important factor in the reduced ginseng yield and quality and soil sickness when ginseng is grown continuously.

Rhizosphere Fungal Dynamics in Sugarcane during Different Growth Stages

Understanding the normal variation of the sugarcane rhizosphere fungal community throughout its life cycle is essential for the development of agricultural practices for fungal and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform for correlation analysis of rhizosphere fungal community time series, covering information from 84 samples in four growth periods. The results revealed that the sugarcane rhizosphere fungi possessed the maximum fungal richness in Tillering. Rhizosphere fungi were closely associated with sugarcane growth, including Ascomycota, Basidiomycota, and Chytridiomycota, which showed high abundance in a stage-specific manner. Through the Manhattan plots, 10 fungal genera showed a decreasing trend throughout the sugarcane growth, and two fungal genera were significantly enriched at three stages of sugarcane growth (p < 0.05) including Pseudallescheria (Microascales, Microascaceae) and Nectriaceae (Hypocreales, Nectriaceae). In addition, soil pH, soil temperature, total nitrogen, and total potassium were critical drivers of fungal community structure at different stages of sugarcane growth. We also found that sugarcane disease status showed a significant and strong negative effect on selected soil properties by using structural equation modeling (SEM), suggesting that poor soil increases the likelihood of sugarcane disease. In addition, the assembly of sugarcane rhizosphere fungal community structure was mainly influenced by stochastic factors, but after the sugarcane root system became stable (Maturity), the stochastic contribution rate decreased to the lowest value. Our work provides a more extensive and solid basis for the biological control of sugarcane potential fungal diseases.

Changes in Fungal and Oomycete Community Composition Following Irrigation Reductions Aimed at Increasing Water Use Efficiency in a Containerized Nursery Crop

Ornamental production in the United States spans an estimated 267,000 ha and uses approximately 169,000 m3 of water yearly. Ornamental growers, particularly those with air-closed systems, are interested in implementing reduced irrigation technologies such as sensor-controlled irrigation systems to improve water use efficiency in response to water scarcity. To evaluate phytobiome impacts, we utilized an Illumina metabarcoding approach to characterize changes in fungal and oomycete rhizosphere communities of commercially grown poinsettia, complementing previous studies of single-pathogen impacts. Minor reductions (from 54 to 50% volumetric water content [VWC]) did not have large effects on rhizosphere fungal community structure but shifts in plant health status (symptomatic to asymptomatic) correlated with shifts in fungal diversity and evenness, with an increased abundance of several taxa, including Plectosphaerella cucumerina and Fusarium spp., in symptomatic plants. Further reductions in irrigation (45, 35, and 25% VWC) did not affect overall fungal community composition but the lowest VWC increased the abundance of potential root rot pathogens such as Phoma multirostrata and Plectosphaerella cucumerina. Reduced irrigation volumes decreased oomycete diversity and abundance of several known pathogens in the Phytophthora genus. Addition of a bacterial product (Companion) with putative pathogen-suppressive and drought-tolerance enhancing effects had no influence on fungal community composition or abundance but did increase abundance of some oomycete species at 45% VWC. This study shows that adoption of reduced irrigation may have greater effects on fungal versus oomycete taxa in the system, with consistent patterns of fungal enhancement, including putative fungal pathogens and beneficial organisms, and oomycete suppression.

Promoting the Growth of Pinus sylvestris var. mongolica Seedlings and Improving Rhizosphere Fungal Community Structure through Interaction between Trichoderma and Ectomycorrhizal Fungi

In this study, pot experiments were conducted on the seedlings of Pinus sylvestris var. mongolica to study the influence of Trichoderma (Trichoderma harzianum E15) and Ectomycorrhizal fungi (Suillus luteus N94) on the growth of these seedlings. In particular, the effects of these fungi on the fungal community structure in the rhizosphere soil of the seedlings were investigated. Inoculation with Trichoderma harzianum E15 and Suillus luteus N94 significantly (P &lt; 0.05) promoted the growth of the Pinus sylvestris seedlings. The non-metric multidimensional scaling (NMDS) results indicated a significant difference (P &lt; 0.05) between the fungal community structures in the rhizosphere soil of the annual and biennial seedlings. In the rhizosphere soil of annual seedlings, the main fungi were Ascomycota, Basidiomycota, Zygomycota. Ascomycota, Basidiomycota, Mortierellomycota, and p-unclassified-k-Fungi were the main fungi in the rhizosphere soil of biennial seedlings. The dominant genus in the rhizosphere soil and a key factor promoting the growth of the annual and the biennial seedlings was Trichoderma, Suillus, respectively. Both of them were negatively correlated with the relative abundance of microbial flora in the symbiotic environment. Trichoderma had a significant promoting effect on the conversion of total phosphorus, total nitrogen, ammonium nitrogen, nitrate nitrogen, and the organic matter in the rhizosphere soil of the seedlings, while Suillus significantly promoted the conversion of organic matter and total phosphorus.

Wheat rhizosphere fungal community is affected by tillage and plant growth

Agricultural management measures, including tillage, considerably alter the rhizosphere fungal community; however, traditional snapshot sampling fail to represent the rhizosphere fungal community patterns over time. Here, we conducted a continuous study of wheat rhizosphere fungal communities through long-term tillage experiments (consisting of conventional and conservation tillage) to clarify tillage and growth stage effects. Tillage practices always affected rhizosphere fungal communities (R2 = 18%), and these effects significantly differed between plant growth stages. Drastic changes in plant phenotypes during the growing season may have driven the changes in rhizosphere fungal communities. Specifically, in the tillering stage (the early period of wheat growth), plant traits dynamics and the abundance of two crop-tillage sensitive modules were highly correlated. The conservation tillage abundant module was mainly composed of saprotrophs, whereas pathogens constituted the majority in modules enriched by conventional tillage. These results indicate that it is possible to influence the rhizosphere fungal community structure and function through agricultural management mediated by plant growth. Manipulation of tillage-sensitive OTUs and early rhizosphere fungal community modules can provide new opportunities for developing sustainable and highly productive agroecosystems.

Application sequence modulates microbiome composition, plant growth and apple replant disease control efficiency upon integration of anaerobic soil disinfestation and mustard seed meal amendment

Anaerobic soil disinfestation (ASD) and mustard seed meal (MSM) amendments can provide effective control of soil-borne diseases including apple replant disease. These measures rely on both chemical and biological modes of action to yield effective disease control and their integration may prove beneficial or, alternatively, deleterious to overall treatment efficiency when applied in concert. Potential outcomes of integrating ASD with MSM amendments were assessed by determining the effect of treatment application sequence and ASD carbon source on generation of allyl isothiocyanate (AITC) derived from Brassica juncea seed meal, structure of the rhizosphere and soil microbiome, control of apple replant pathogens, and plant growth. In bioassays conducted using ‘Gala’ apple seedlings, application of ASD or MSM treatments independently was as effective or superior to all integrated treatments for the control of replant pathogens. Application of ASD prior to MSM amendment diminished the yield of AITC attained in response to soil incorporation of the Brassica juncea:Sinapis alba seed meal. Treatment application sequence had significant effect on structure of the bulk soil fungal and bacterial community. Correspondingly, treatment application sequence significantly altered plant growth performance when orchard grass was utilized as the ASD carbon input. At harvest, rhizosphere fungal but not bacterial community composition was significantly altered in treated soil relative to the control, and sequence of treatment application had significant effect on rhizosphere fungal community structure. Failure of integrated treatments to enhance overall replant disease control may have resulted from many factors including reduced generation of active metabolites, diminished activity of mechanisms functional in pathogen suppression, or the elevated accumulation and retention of phytotoxic chemistries, the latter which would require extended plant back periods to circumvent. The findings indicate that under the experimental conditions employed, integration of ASD with MSM amendment is unlikely to yield additive or synergistic effects on apple replant disease control.

Rhizobium Inoculation Drives the Shifting of Rhizosphere Fungal Community in a Host Genotype Dependent Manner.

Rhizosphere microorganisms play important roles in plant health and nutrition, and interactions among plants and microorganisms are important for establishment of root microbiomes. As yet, plant-microbe and microbe-microbe interactions in the rhizosphere remain largely mysterious. In this study, rhizosphere fungal community structure was first studied in a field experiment with two soybean cultivars contrasting in nodulation grown in two rhizobium inoculation treatments. Following this, recombinant inbred lines (RILs) contrasting in markers across three QTLs for biological nitrogen fixation (BNF) were evaluated for effects of genotype and rhizobium inoculation to the rhizosphere fungal community as assessed using ITS1 amplicon sequencing. The soybean plants tested herein not only hosted rhizosphere fungal communities that were distinct from bulk soils, but also specifically recruited and enriched Cladosporium from bulk soils. The resulting rhizosphere fungal communities varied among soybean genotypes, as well as, between rhizobium inoculation treatments. Besides, Cladosporium were mostly enriched in the rhizospheres of soybean genotypes carrying two or three favorable BNF QTLs, suggesting a close association between soybean traits associated with nodulation and those affecting the rhizosphere fungal community. This inference was bolstered by the observation that introduction of exogenous rhizobia significantly altered rhizosphere fungal communities to the point that these communities could be distinguished based on the combination of soybean genotype and whether exogenous rhizobia was applied. Interestingly, grouping of host plants by BNF QTLs also distinguished fungal community responses to rhizobium inoculation. Taken together, these results reveal that complex cross-kingdom interactions exist among host plants, symbiotic N2 fixing bacteria and fungal communities in the soybean rhizosphere.

Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton.

Rhizosphere fungal communities exert important influencing forces on plant growth and health. However, information on the dynamics of the rhizosphere fungal community structure of the worldwide economic crop cotton (Gossypium spp.) is limited. In the present study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 (ITS1) was performed to characterize the rhizosphere fungal communities of G. hirsutum cv. TM-1 (upland cotton) and G. barbadense cv. Hai 7124 (island cotton). The plants were grown in field soil (FS) that had been continuously cropped with cotton and nutrient-rich soil (NS) that had not been cropped. The fungal species richness, diversity, and community composition were analyzed and compared among the soil resources, cotton genotypes, and developmental stages. We found that the fungal community structures were different between the rhizosphere and bulk soil and the difference were significantly varied between FS and NS. Our results suggested that cotton rhizosphere fungal community structure variation may have been primarily influenced by the interaction of cotton roots with different soil resources. We also found that the community composition of the cotton rhizosphere fungi varied significantly during different developmental stages. In addition, we observed fungi that was enriched or depleted at certain developmental stages and genotypes in FS and NS, and these insights can lay a foundation for deep research into the dynamics of pathogenic fungi and nutrient absorption of cotton roots. This research illustrates the characteristics of the cotton rhizosphere fungal communities and provides important information for understanding the potential influences of rhizosphere fungal communities on cotton growth and health.

Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage

Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H+-ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety. Real-time quantitative PCR analysis confirmed a significant rise in the richness of Cladosporium cladosporioides in esl mutant rice than the wild type variety. Correlation analysis revealed four most abundant genera identified for the esl mutant and their close association with yield and biomass decline, lipid peroxidation, lower root vitality, chlorophyll degradation and limited VHA activity. Higher K+ efflux, H+ and a lower Ca2+ influx was also observed in the esl mutant which could be the reason for abnormal functioning of mutant plants. These results illustrate that besides the well-known effect of senescence on plant physiology and yield decline, it can further shape the rhizosphere fungal community.

Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton

The large-scale long-term plantation of cotton in the Xinjiang region has been accompanied by a regular and wide outbreak of soil-borne fungal diseases such as verticillium wilt, which significantly damaged the local cotton industry. High-throughput sequencing data showed that the cotton field cultivation management measures pose a significant influence upon the original ecological soil fungal community structure. During long-term continuous cropping of cotton, a new soil fungal community structure emerges after several repeated adjustments over five years. The number of verticillium wilt pathogens in the soil increased rapidly with prolonged continuous cropping time, reaching a maximum at around the 10th y; moreover, the abundance of the verticillium wilt pathogen only serves as one of numerous essential factors for disease occurrence. The fungal community structure and the abundance of verticillium wilt pathogens in local cotton fields are gradually formed under joint effects of year-long continuous cropping and supporting cultivation management measures.

Responses of Soil Microbial Communities in the Rhizosphere of Cucumber (Cucumis sativus L.) to Exogenously Applied p-Hydroxybenzoic Acid

Changes in soil biological properties have been implicated as one of the causes of soil sickness, a phenomenon that occurs in continuous monocropping systems. However, the causes for these changes are not yet clear. The aim of this work was to elucidate the role of p-hydroxybenzoic acid (PHBA), an autotoxin of cucumber (Cucumis sativus L.), in changing soil microbial communities. p-Hydroxybenzoic acid was applied to soil every other day for 10 days in cucumber pot assays. Then, the structures and sizes of bacterial and fungal communities, dehydrogenase activity, and microbial carbon biomass (MCB) were assessed in the rhizosphere soil. Structures and sizes of rhizosphere bacterial and fungal communities were analyzed by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time PCR, respectively. p-Hydroxybenzoic acid inhibited cucumber seedling growth and stimulated rhizosphere dehydrogenase activity, MBC content, and bacterial and fungal community sizes. Rhizosphere bacterial and fungal communities responded differently to exogenously applied PHBA. The PHBA decreased the Shannon-Wiener index for the rhizosphere bacterial community but increased that for the rhizosphere fungal community. In addition, the response of the rhizosphere fungal community structure to PHBA acid was concentration dependent, but was not for the rhizosphere bacterial community structure. Our results indicate that PHBA plays a significant role in the chemical interactions between cucumber and soil microorganisms and could account for the changes in soil microbial communities in the continuously monocropped cucumber system.

Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings

Mine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length ( p < 0.05) and effective AMF colonization compared to controls grown in uninoculated compost-amended tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by AMF, or a combination of both mechanisms.

Plant defence against nematodes is not mediated by changes in the soil microbial community

1 Indirect plant defence, the recruitment of antagonists of herbivores, is well-known above the ground. In spite of various soil microorganisms acting as antagonists to root herbivores, it is still largely unknown whether plants can promote antagonistic microorganisms as an indirect defence mechanism. 2 In a greenhouse study we examined whether soil microorganisms could mediate plant defence against plant-feeding nematodes. Growth, nutrient contents and root exudation of three plant species (Plantago lanceolata, Holcus lanatus, Lotus corniculatus) and the performance of nematodes and fungal communities in the rhizospheres were measured. 3 The plant species differed in their effects on plant-feeding nematodes; however, the addition of soil microorganisms did not enhance nematode control. Nematode addition changed root exudation patterns and rhizosphere fungal community structure in a plant species-specific manner. Glucose levels in the root exudates of all three examined plant species were enhanced, and P. lanceolata root exudates contained higher levels of fumaric acid when nematodes had been added. 4 We conclude that nematodes have plant species-specific effects on root exudate chemistry and rhizosphere fungal community composition, but these effects do not necessarily enhance indirect control of nematodes by antagonistic microorganisms. More studies on below-ground plant defence are definitely needed.