Rhizosphere microbial ecological characteristics of strawberry root rot

Involvement of the SIX10 Gene in the Pathogenicity of Fusarium oxysporum Formae Speciales in Strawberries

Strawberries are planted globally as an important crop. Fusarium oxysporum f. sp. fragariae (Fof), a haploid mitosporic, pathogenic fungus with obvious host specificity, is responsible for an economically devastating soil-borne disease seriously threatening strawberry. Fusarium oxysporum is distributed in soils worldwide and causes vascular wilt and root rot disease in over 100 plant species. However, the formae speciales of F. oxysporum commonly have a very narrow host range, often restricted to a single host plant species. We isolated and identified pathogenic F. oxysporum from diseased strawberry samples collected from different provinces in China. Further analysis showed that among the 55 F. oxysporum isolates, only 70.91% belonged to Fof, and the remaining 29.09% were named Fo. The mycelial growth of Fof was faster than that of Fo at 20, 30, and 35 °C. The sporulation ability of Fof was weaker than that of Fo, and Fof presented a significantly higher germination rate under high temperatures. Fof and Fo from strawberry were not pathogenic to tomato or cucumber plants, and Fof showed significantly higher pathogenicity on strawberry than Fo. To explore the pathogenic mechanism of Fof, we knocked out SIX10 in Fof. The mycelial growth rate of ΔFofSIX10 was significantly slower than that of the wild type, but there were no significant differences in spore production. The pathogenicity of ΔFofSIX10 to strawberry was significantly weakened, showing decreased severity of symptoms, indicated by root and crown rot, and wilt. Our research provides a basis for understanding the interaction between F. oxysporum and the host strawberry and the occurrence and management of Fusarium disease on strawberry.

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.

Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.

A Novel Plant-Derived Biopesticide Mitigates Fusarium Root Rot of Angelica sinensis by Modulating the Rhizosphere Microbiome and Root Metabolome

Fusarium root rot caused by the Fusarium species complex significantly affects the yield and quality of Angelica sinensis, a valuable medicinal herb. Traditional management primarily relies on chemical fungicides, which have led to pathogen resistance, environmental hazards, and concerns regarding public health and the active components in A. sinensis. This study explores the efficacy of a novel plant-derived biopesticide Shi Chuang Zhi Feng Ning (T1; SCZFN), alongside Bacillus subtilis wettable powder (T2) and a chemical fungicide (T3), in controlling root rot and understanding their impacts on the rhizosphere microbial community and root metabolome. Results of the field experiment demonstrated that treatments T1 and T3 achieved control efficiencies of 73.17% and 75.45%, respectively, significantly outperforming T2 (39.99%) and the control. High-throughput sequencing revealed that all treatments altered the diversity and structure of microbial communities, with T1 and T2 reducing the abundance of taxa linked to root rot, such as Muribaculaceae spp., Humicola spp., Fusarium spp., and Mycochlamys spp. Treatment T1 notably enhanced beneficial bacterial taxa, including Acidobacteria spp., Nitrospira spp., and Pedosphaeraceae spp., involved in carbon cycling and plant growth promotion. Metabolomic analysis identified 39, 105, and 45 differentially expressed metabolites (DEMs) across the treatments, demonstrating T1's potential to modulate the root metabolome effectively. Further, a correlation analysis demonstrated a stronger correlation between distinct microorganisms with significant influence and DEMs of T1 treatment compared to other treatments. These findings underscore biopesticide SCZFN's role in enhancing plant health and disease suppression in A. sinensis, providing insights into its biocontrol mechanisms and supporting the development of sustainable disease management strategies in its cultivation.

Biological Control of Root Rot of Strawberry by Bacillus amyloliquefaciens Strains CMS5 and CMR12

Strawberry root rot caused by Fusarium solani is one of the main diseases of strawberries and significantly impacts the yield and quality of strawberry fruit. Biological control is becoming an alternative method for the control of plant diseases to replace or decrease the application of traditional chemical fungicides. To obtain antagonistic bacteria with a high biocontrol effect on strawberry root rot, over 72 rhizosphere bacteria were isolated from the strawberry rhizosphere soil and screened for their antifungal activity against F. solani by dual culture assay. Among them, strains CMS5 and CMR12 showed the strongest inhibitory activity against F. solani (inhibition rate 57.78% and 65.93%, respectively) and exhibited broad-spectrum antifungal activity. According to the phylogenetic tree based on 16S rDNA and gyrB genes, CMS5 and CMR12 were identified as Bacillus amyloliquefaciens. Lipopeptide genes involved in surfactin, iturin, and fengycin biosynthesis were detected in the DNA genomes of CMS5 and CMR12 by PCR amplification. The genes related to the three major lipopeptide metabolites existed in the DNA genome of strains CMS5 and CMR12, and the lipopeptides could inhibit the mycelial growth of F. solani and resulted in distorted hyphae. The inhibitory rates of lipopeptides of CMS5 and CMR12 on the spore germination of F. solani were 61.00% and 42.67%, respectively. The plant-growth-promoting (PGP) traits in vitro screening showed that CMS5 and CMR12 have the ability to fix nitrogen and secreted indoleacetic acid (IAA). In the potting test, the control efficiency of CMS5, CMR12 and CMS5+CMR12 against strawberry root rot were 65.3%, 67.94% and 88.00%, respectively. Furthermore, CMS5 and CMR12 enhanced the resistance of strawberry to F. solani by increasing the activities of defense enzymes MDA, CAT and SOD. Moreover, CMS5 and CMR12 significantly promoted the growth of strawberry seedlings such as root length, seedling length and seedling fresh weight. This study revealed that B. amyloliquefaciens CMS5 and CMR12 have high potential to be used as biocontrol agents to control strawberry root rot.

Trichoderma harzianum prevents red kidney bean root rot by increasing plant antioxidant enzyme activity and regulating the rhizosphere microbial community

Root rot is one of the main reasons for yield losses of red kidney bean (Phaseolus vulgaris) production. Pre-inoculation with Trichoderma harzianum can effectively lower the incidence of red kidney bean root rot. In this study, four treatments including CK (control), Fu13 (Fusarium oxysporum), T891 (T. harzianum) and T891 + Fu13 (T. harzianum + F. oxysporum) were arranged in a pot experiment to investigate how T891 affected the incidence and severity of root rot, plant growth, and changes of defense enzyme activity in red kidney bean plants. Community composition and diversity of the rhizosphere microbiota was evaluated through high-throughput sequencing, and co-occurrence network was analyzed. The results showed that when compared to the Fu13 treatment, pre-inoculation with T891 reduced the incidence and severity of red kidney bean root rot by 40.62 and 68.03% (p < 0.05), increased the root length, shoot length, total dry biomass by 48.63, 97.72, 122.17%. Upregulated activity of super-oxide dismutase (SOD), peroxidase (POD), catalase (CAT) by 7.32, 38.48, 98.31% (p < 0.05), and reduced malondialdehyde (MDA) by 23.70% (p < 0.05), respectively. Microbiological analyses also showed that F. oxysporum reduced alpha diversity resulting in alteration the composition of the rhizosphere microbial community in red kidney bean. T891 significantly reduced abundance of F. oxysporum, allowing the enrichment of potentially beneficial bacteria Porphyrobacter (ASV 46), Lysobacter (ASV 85), Microbacteriaceae (ASV 105), and Gemmatimonas (ASV 107), resulting in a more stable structure of the microbial network. The results of random forest analysis further revealed that ASV 46 (Porphyrobacter) was the primary influencing factor for the incidence of root rot after inoculation with T891, while ASV 85 (Lysobacter) was the primary influencing factor for the biomass of red kidney bean. In conclusion, T. harzianum promotes the growth of red kidney bean and inhibits root rot by improving plant antioxidant enzyme activity and regulating the rhizosphere microbial community.