Nitrate Stabilizes the Rhizospheric Fungal Community to Suppress Fusarium Wilt Disease in Cucumber

Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

Rhizosphere microbial ecological characteristics of strawberry root rot

Introduction

Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.

Methods

In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.

Results

According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.

Discussion

In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.

Harnessing nitrate over ammonium to sustain soil health during monocropping

Introduction

In achieving food security and sustainable agricultural development, improving and maintaining soil health is considered as a key driving factor. The improvement based on different forms of nitrogen fertilization has aroused great public interest in improving and restoring monocropping obstacles for specific soil problems.

Methods

For this, a short-term cucumber cropping field experiment was conducted in the subtropical region of China under four fertilization treatments: ammonium (AN), nitrate (NN), ammonium with dicyandiamide (AN+DCD), nitrate with dicyandiamide (NN+DCD). In this study, we measured the effects of nitrogen forms addition on plant productivity and soil health in a monocropping system over seven seasons.

Results

To systematically evaluate soil health, a wide range of soil environmental factors were measured and incorporated into the soil health index (SHI) by entropy method. Compared with ammonium treatment (SHI_AN = 0.059, SHI_AN+DCD = 0.081), the positive effect of nitrate was mainly reflected in improving soil health (SHI_NN = 0.097, SHI_NN+DCD = 0.094), which was positively correlated with the increase in plant productivity of cucumber after seven seasons of monocropping. The most critical factor affecting SHI is soil ammonium nitrogen content, which was negatively correlated with plant productivity.

Discussion

Nitrate promotes soil health and plant productivity by optimizing soil environmental factors. The study thus emphasized the necessity of nitrate input for the sustenance of soil-crop ecosystems, with the consequent possibility of application of the results in planning monoculture obstacle prevention and management measures.

15N tracing reveals preference for different nitrogen forms of Fusarium oxysporum f. sp. cubense tropical race 4

Plant uptake of nitrogen is often associated with increased incidence of banana Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). However, the nitrogen metabolic preferences of Foc TR4 pathogens remain unknown. In this study, we investigated the ecophysiological patterns of Foc TR4 grown on different combinations of organic and inorganic nitrogen. Potato Dextrose Agar (PDA) and Rose Bengal Medium (RBM) were used as an organic nitrogen source, which was sequentially replaced with inorganic N (0, 50% or 90%) in the form ¹⁵NH₄NO₃ or NH₄ ¹⁵NO₃ to reveal preferential assimilation of ammonium or nitrate. The results showed that mycelium biomass and nitrogen content decreased significantly, while the carbon content and C:N ratio increased in Foc TR4 grown on media containing inorganic nitrogen sources. Mycelium biomass was negatively correlated with C:N ratio. Mycelium ¹⁵N abundance increased significantly between the PDA50 + A50/RBM50 + A50 treatments (50% organic nitrogen+50%¹⁵NH₄NO₃) and the PDA10 + A90/RBM10 + A90 treatments (10% organic nitrogen+90%¹⁵NH₄NO₃). These results indicate that the higher C:N ratio reduced mycelium growth by reducing its biomass and diameter and showed that Foc TR4 preferred to use ammonium nitrogen to promote the growth. These findings suggest that treating banana crops with a combination of organic and inorganic (i.e., nitrate) nitrogen could be a better way to defend against Fusarium wilt of banana.

Ammonium fertilization increases the susceptibility to fungal leaf and root pathogens in winter wheat

Nitrogen (N) fertilization is indispensable for high yields in agriculture due to its central role in plant growth and fitness. Different N forms affect plant defense against foliar pathogens and may alter soil-plant-microbe interactions. To date, however, the complex relationships between N forms and host defense are poorly understood. For this purpose, nitrate, ammonium, and cyanamide were compared in greenhouse pot trials with the aim to suppress two important fungal wheat pathogens Blumeria graminis f. sp. tritici (Bgt) and Gaeumannomyces graminis f. sp. tritici (Ggt). Wheat inoculated with the foliar pathogen Bgt was comparatively up to 80% less infested when fertilized with nitrate or cyanamide than with ammonium. Likewise, soil inoculation with the fungal pathogen Ggt revealed a 38% higher percentage of take-all infected roots in ammonium-fertilized plants. The bacterial rhizosphere microbiome was little affected by the N form, whereas the fungal community composition and structure were shaped by the different N fertilization, as revealed from metabarcoding data. Importantly, we observed a higher abundance of fungal pathogenic taxa in the ammonium-fertilized treatment compared to the other N treatments. Taken together, our findings demonstrated the critical role of fertilized N forms for host-pathogen interactions and wheat rhizosphere microbiome assemblage, which are relevant for plant fitness and performance.

Endophytic Fungal and Bacterial Microbiota Shift in Rice and Barnyardgrass Grown under Co-Culture Condition

Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during co-planted barnyardgrass stress and a comparison with the microbiomes of unplanted soil, we found that the bacterial community diversity of rice was dramatically higher while the fungal community richness was significantly lower than that of barnyardgrass at BBCH 45 and 57. More importantly, rice recruited more endophytic bacteria at BBCH 45 and 57, and more endophytic fungi at BBCH 17, 24, 37 to aginst the biotic stress from barnyardgrass. Principal coordinates analysis (PCoA) showed that rice and barnyardgrass had different community compositions of endophytic bacteria and fungi in roots. The PICRUSt predictive analysis indicated that majority of metabolic pathways of bacteria were overrepresented in barnyardgrass. However, eleven pathways were significantly presented in rice. In addition, rice and barnyardgrass harbored different fungal trophic modes using FUNGuild analysis. A negative correlation between bacteria and fungi in rice and barnyardgrass roots was found via network analysis. Actinobacteria was the vital bacteria in rice, while Proteobacteria dominated in barnyardgrass, and Ascomycota was the vital fungi in each species. These findings provided data and a theoretical basis for the in-depth understanding of the competition of barnyardgrass and endophytes and have implications relevant to weed prevention and control strategies using root microbiota.

Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities

Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.

Identification of Susceptibility Genes for Fusarium oxysporum in Cucumber via Comparative Proteomic Analysis

Fusarium wilt (FW) in cucumber (Cucumis sativus L.), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), poses a major threat to cucumber growth and productivity. However, lack of available natural resistance resources for FW restricts the breeding of resistant cultivars via conventional approaches. Susceptibility (S) genes in susceptible host plants facilitate infection by the pathogen and contribute to susceptibility. Loss of function of these S genes might provide broad-spectrum and durable disease resistance. Here, we screened S genes via comparative proteomic analysis between cucumber cultivars Rijiecheng and Superina, which exhibited resistance and high -susceptibility to FW, respectively. We identified 210 and 243 differentially regulated proteins (DRPs) in the Rijiecheng and Superina, respectively, and further found that 32 DRPs were predominantly expressed in Superina and significantly up-regulated after Foc inoculation. Expression verification found that TMEM115 (CsaV3_5G025750), encoding a transmembrane protein, TET8 (CsaV3_2G007840), encoding function as a tetraspanin, TPS10 (CsaV3_2G017980) encoding a terpene synthase, and MGT2 (CsaV3_7G006660), encoding a glycosyltransferase, were significantly induced in both cultivars after Foc infection but were induced to a higher expression level in Superina. These candidate genes might act as negative regulators of FW resistance in cucumber and provide effective FW-susceptibility gene resources for improving cucumber FW resistance through breeding programs.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Pythium spp. Associated with Root Rot and Stunting of Winter Wheat in North Carolina

In eastern North Carolina, mild to severe stunting and root rot have reduced yields of winter wheat, especially during years with abundant rainfall. Causal agents of root rot of wheat in this region were previously identified as Pythium irregulare, P. vanterpoolii, and P. spinosum. To investigate species prevalence, 114 isolates of Pythium were obtained from symptomatic wheat plants collected in eight counties. Twelve species were recovered, with P. irregulare (32%), P. vanterpoolii (17%), and P. spinosum (16%) the most common. Pathogenicity screens were performed with selected isolates of each species, and slight to severe necrosis of young roots was observed. The aggressiveness of five isolates each of P. irregulare, P. vanterpoolii, and P. spinosum was compared on a single cultivar of wheat at 14°C, and very aggressive isolates were found within all species. In vitro growth of these isolates was measured at 14 and 20°C, and all isolates grew faster at the warmer temperature. The effects of varying temperatures and rates of nitrogen on root rot caused by Pythium spp. alone or in combination were investigated. All inoculation treatments caused severe root rot under all conditions tested, and disease was more severe at 12 and 14°C compared with 18 and 20°C; however, there was no effect of nitrogen application.

Dragonfly-Associated Trichoderma harzianum QTYC77 Is Not Only a Potential Biological Control Agent of Fusarium oxysporum f. sp. cucumerinum But Also a Source of New Antibacterial Agents

A strain isolated from the gut of Pantala flavescens was characterized as Trichoderma harzianum QTYC77. The strain was assessed as a potential biocontrol agent against Fusarium oxysporum f. sp. cucumerinum (FOC). Mycoparasitism and competing abilities of T. harzianum QTYC77 lead to inhibition of the mycelial growth of FOC, with the inhibition rate of 70.99%, in dual culture assays. Activities of chitinase and β-1,3-glucanase, responsible for fungal cell-wall degradation, were gradually increased and their activities were the maximum on the fifth day of fermentation with 23.20 and 1.84 U/mL, respectively. T. harzianum QTYC77 was discovered to have potent biocontrol potential with the control efficiency of 67.43% against the FOC in vivo pot experiment. Furthermore, two novel compounds azaphilone D (1) and E (2) along with three known metabolites 3-hydroxymethyl-6, 8-dimethoxycoumarin (3), harzianone (4), and pachybasin (5) were isolated and identified from T. harzianum QTYC77. Unfortunately, these metabolites did not show antifungal activities against FOC. However, both metabolites 1 and 3 displayed moderate activity against Staphylococcus aureus with disc diameters of zone of inhibition (ZOI) of 7.3 and 7.2 mm, respectively, compared with that of referenced gentamycin (ZOI = 14.5 mm). In addition, metabolite 1 possessed a moderate antibacterial activity against Bacillus subtilis with a ZOI value of 7.0 mm compared with that of positive gentamycin (ZOI = 15.2 mm). The present results suggested that T. harzianum QTYC77 was not only a potential biofungicide against FOC but also the source of new antibacterial agents.

Organic Fertilization Assembles Fungal Communities of Wheat Rhizosphere Soil and Suppresses the Population Growth of Heterodera avenae in the Field

Heterodera avenae (cereal cyst nematode, CCN) infects wheat and other cereal crops and causes severe losses in their yield. Research has shown that CCN infestations can be mitigated by organic fertilization in wheat fields, but the mechanisms underlying this phenomenon are still largely unknown. In this study, the relationships among CCN, soil properties, and soil fungal communities with organic fertilizer (OF) or chemical fertilizer (CF) and without fertilizer (CK), were investigated for two years in a wheat field in Henan province, China. Our results showed that the concentrations of soil total N, total P, available P, available K, and organic matter were all promoted by the OF treatment at the jointing stage of wheat, coinciding with the peak in egg hatching and penetration of wheat root by CCNs. Soil total N correlated positively (R² = 0.759, p < 0.05) with wheat yields but negatively (R² = 0.663, p < 0.01) with Pf/Pi (index of cyst nematode reproduction), implying the regulated soil property contributes to suppressing CCN in the OF treatment. Furthermore, fungal community α-diversity (Shannon and Simpson) and β-diversity (PCoA) of rhizosphere soil was improved under the organic fertilizer treatment. The fungal genera negatively associated with the Pf/Pi of CCN were highly enriched, which included Mortierella and Chaetomium, two taxa already reported as being nematophagous fungi in many other studies. These two genera were heavily surrounded by much more related fungal genera in the constructs co-occurrence network. These results suggested that the OF treatment shifted soil fungal community functioning towards the suppression of CCN. Taken together, the suppressed cyst nematode reproduction with the assembly of fungal communities in the rhizosphere led to greater wheat yields under organic fertilization. These findings provide an in-depth understanding of the benefits provided by organic fertilization for developing sustainable agriculture.