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Background Plant health and growth are negatively affected by pathogen invasion; however, plants can dynamically modulate their rhizosphere microbiome and adapt to such biotic stresses. Although plant-recruited protective microbes can be assembled into synthetic communities for application in the control of plant disease, rhizosphere microbial communities commonly contain some taxa at low abundance. The roles of low-abundance microbes in synthetic communities remain unclear; it is also unclear whether all the microbes enriched by plants can enhance host adaptation to the environment. Here, we assembled a synthetic community with a disease resistance function based on differential analysis of root-associated bacterial community composition. We further simplified the synthetic community and investigated the roles of low-abundance bacteria in the control of Astragalus mongholicus root rot disease by a simple synthetic community. Results Fusarium oxysporum infection reduced bacterial Shannon diversity and significantly affected the bacterial community composition in the rhizosphere and roots of Astragalus mongholicus . Under fungal pathogen challenge, Astragalus mongholicus recruited some beneficial bacteria such as Stenotrophomonas , Achromobacter , Pseudomonas , and Flavobacterium to the rhizosphere and roots. We constructed a disease-resistant bacterial community containing 10 high- and three low-abundance bacteria enriched in diseased roots. After the joint selection of plants and pathogens, the complex synthetic community was further simplified into a four-species community composed of three high-abundance bacteria ( Stenotrophomonas sp., Rhizobium sp., Ochrobactrum sp.) and one low-abundance bacterium ( Advenella sp.). Notably, a simple community containing these four strains and a thirteen-species community had similar effects on the control root rot disease. Furthermore, the simple community protected plants via a synergistic effect of highly abundant bacteria inhibiting fungal pathogen growth and less abundant bacteria activating plant-induced systemic resistance. Conclusions Our findings suggest that bacteria with low abundance play an important role in synthetic communities and that only a few bacterial taxa enriched in diseased roots are associated with disease resistance. Therefore, the construction and simplification of synthetic communities found in the present study could be a strategy employed by plants to adapt to environmental stress. -VujMZjCpFzTumqS8Rf9nH Video abstract

Background In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant–microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola -mediated black root rot of tobacco, to test the hypothesis that plant–microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses. Results Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives. Conclusions Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.

Background and aims Root rot is a catastrophic disease of perennial medicinal plants which could be caused by various soil-borne fungal pathogens. However, the understanding of the composition and diversity of root rot pathogenic fungi, their successions and potential drivers remains limited. Methods Sanqi ginseng ( Panax notoginseng ) was selected as a model plant and the rhizosphere soils of root rot-infected Sanqi ginseng at different growth years were collected. Phenolic acid content, pathogen abundance, and fungal microbiota were examined by using the high-performance liquid chromatography (HPLC), real-time PCR and Miseq sequencing. Results Pathogenic agents dominated in the rhizospheric fungal microbiota of rotten Sanqi ginseng and mainly comprised of Ilyonectria , Plectosphaerella , Clonostachys , Gibberella , Pestalotiopsis , Fusarium , and Chalara , with Ilyonectria and Fusarium being most abundant. The composition of pathogenic microbiota, but not α-diversity indices, changed considerably with Sanqi ginseng growth. The shifts of phenolic acid profile were an important driver in changes of rhizosphere pathogenic microbiota, and same phenolic acid exerted distinct functions on differential pathogenic taxa. Particularly, the contents of p -coumaric acid, ferulic acid, and benzoic acid were positively correlated with the abundance of genus Fusarium and negatively correlated with the abundance of genus Ilyonectria . Conclusions Root rot-infected Sanqi ginseng rhizosphere harbors dynamically pathogenic microbiota driven by the shift of phenolic acids. This study provides insights into the composition, variation, and driver of root rot pathogenic microbiota; these insights are important for the development of targeted measure for the prevention and control of root rot diseases.

Soil sterilization integrated with agronomic measures is an effective method to reduce soilborne replant diseases. However, the effect of vermicompost or biochar application after soil sterilization on soilborne diseases is poorly understood. A pot experiment was conducted in American ginseng to investigate the effects of vermicompost (VF), biochar (BF), and a combination of vermicompost and biochar (VBF) applied after soil sterilization on the incidence of Fusarium root rot using natural recovery (F) as control. After one growing season, the disease index of root rot, the phenolic acids, and the microbial communities of American ginseng rhizosphere soil were analyzed. The disease index of VF, BF, and VBF decreased by 33.32%, 19.03%, and 80.96%, respectively, compared with F. The highest bacterial richness and diversity were observed in the rhizosphere soil of VBF. Besides, VF and VBF significantly increased the relative abundance of beneficial bacteria (Pseudomonas, Lysobacter, and Chryseolinea) in the rhizosphere soil. Higher concentrations of vanillin, one of the phenolic acids in the roots exudates, were recorded in the rhizosphere soils of BF and VBF. The vanillin concentration showed a significant negative correlation with the disease index. To conclude, vermicompost improved the beneficial bacteria of the rhizosphere soil, while biochar regulated the allelopathic effect of the phenolic acids. The study proposes a combined application of biochar and vermicompost to the rhizosphere soil to control Fusarium root rot of replanted American ginseng effectively.Key pointsVermicompost improves the relative abundance of rhizosphere beneficial bacteria.Biochar inhibits the degradation of phenolic acids by adsorption.The combination of vermicompost and biochar enhances the disease control effect.

Cassava (Manihot esculenta Crantz) is a major staple food in many developing countries, including Brazil. However, it faces significant challenges due to diseases such as dry root rot (DRR) and black root rot (BRR) caused by soil-borne plant pathogenic fungi. This study explored the use of cover crops to suppress these diseases and to improve the agronomic traits of cassava. Over four cultivation cycles, various cover crops (sunn hemp, black oat, jack bean, maize, peanut and cowpea) were alternated with cassava varieties 'BRS Kiriris' (resistant) and 'BRS Formosa' (susceptible) in soil infested with DRR (Fusarium oxysporum, F. equiseti, F. verticillioides, F. solani, F. lateritium, F. chlamydosporum) and BRR (Lasiodiplodia theobramae, Neoscytalidium dimidiatum) pathogens. In the 2nd cycle, only germination showed significant differences, but by the 4th cycle, various agronomic parameters, including fresh weight (FW.AP), dry weight (DW.AP) of the aerial part, fresh weight (FW.Root), dry weight (DW.Root) of the roots, and plant vigor. Cowpea was identified as the most effective cover crop for reducing the disease index (DI %) by promoting healthier and taller cassava plants. Jack beans and peanuts also had positive effects on vigor, FW.AP, DW.AP, FW.root, and DW.root. In contrast, maize, black oats, Crotalaria ochroleuca, cassava, and fallow soils had minimal impacts. Throughout these cycles, the selected cover crops consistently contributed to disease reduction and improved the agronomic performance of the cassava. This study highlights the potential of holistic disease management strategies.

The effectiveness of Trichoderma viride and Bacillus subtilis to protect strawberry against black root rot disease under the greenhouse and field conditions was investigated. In in vitro bioassays, the two microorganisms exhibited strong capabilities to antagonize the pathogen Rhizoctonia fragariae. Soil amendment with T. viride at rate 50 ml/ plant (1 x 107/ ml) conidial spore and B. subtilis at rate 50 ml/ plant (1 x 108 / ml cfu) separately or in combination ameliorated the disease symptoms, enhanced plant growth parameters reaching 1.2 and 1.6 fold for shoot and root growth in greenhouse, whereas the growth enhancement reached 1.2 and 1.5 fold for shoot and roots growth in the field. Consequently, fruit numbers was increased by 2 and 4 fold for plants grown in the greenhouse and fields , respectively. Further biochemical evaluation revealed a substantial increase in ethylene signals at day 2 and 4 and remained high at day 7 after treatment under greenhouse and field conditions, whereas the accumulation of hydrogen peroxide (H2O2) was decreased at day 2 after treatment compared with pathogen infected plants. Furthermore, T. viride and B. subtilis application ameliorated ion leakage damage in infected plants whereas lipid peroxidation decreased significantly resulting in maintaining cell membrane integrity. In addition, examination of the capability of the two microorganisms to enhance the antioxidant enzymatic activities exhibited a significant increase of superoxide dismutase (SOD) and catalase (CAT) activities on day 4, 5 and 6 after treatments. These results suggest that the application of T. viride and B. subtilis as soil amendment provides a significant protection against R. fragariae and improves plant growth parameters and fruit numbers. However, the combination of the two bioagents did not provide additional protection.

Root rot disease caused by Fusarium oxysporum is a devastating disease of Salvia miltiorrhiza and dramatically affected the production and quality of Sa. miltiorrhiza . Besides the agricultural and chemical control, biocontrol agents can be utilized as an additional solution. In the present study, an actinomycete that highly inhibited F. oxysporum was isolated from rhizosphere soil and identified as based on morphological and molecular characteristics. Greenhouse assay proved that the strain had significant biological control effect against Sa. miltiorrhiza root rot disease and growth-promoting properties on Sa. miltiorrhiza seedlings. To elucidate the biocontrol and plant growth-promoting properties of St-220, we employed an analysis combining genome mining and metabolites detection. Our analyses based on genome sequence and bioassays revealed that the inhibitory activity of St-220 against F. oxysporum was associated with the production of enzymes targeting fungal cell wall and metabolites with antifungal activities. Strain St-220 possesses phosphate solubilization activity, nitrogen fixation activity, siderophore and indole-3-acetic acid production activity in vitro , which may promote the growth of Sa. miltiorrhiza seedlings. These results suggest that St. albidoflavus St-220 is a promising biocontrol agent and also a biofertilizer that could be used in the production of Sa. miltiorrhiza .

Armillaria solidipes, the causal agent of Armillaria root rot, poses a severe and persistent threat to poplar forest plantations. This study evaluated the biocontrol efficacy of the endophytic bacterium Bacillus velezensis BY6 against this pathogen and elucidated its multimodal mechanisms of action. BY6 application significantly reduced disease severity by 37.19% at 30 days post-treatment. 16S rRNA (V3–V4) microbiome analysis revealed that BY6 reshaped both the rhizosphere and phyllosphere bacterial communities, consistently enriching beneficial taxa, including Pantoea ananatis and members of Acidobacteria, while suppressing opportunistic groups. Concurrently, BY6 activated systemic defenses in poplar, evidenced by enhanced activities of key enzymes PAL and POD, and the upregulated expression of SA/JA pathway marker genes (PR1, JAZ, and COI1), coupled with the downregulation of the auxin transporter gene AUX1. These data indicate that the biocontrol efficacy of B. velezensis BY6 was mediated by a dual mechanism: the modulation of both rhizospheric and phyllospheric bacterial communities, direct elicitation of systemic defense pathways in poplar, which synergistically enhanced resistance against A. solidipes.

Background Faba bean (Vicia faba L.) cultivation is highly challenged by faba bean black root rot disease (Fusarium solani) in high lands of Ethiopia. To ensure sustainable production of faba beans, searching for eco-friendly disease management options is necessary to curb the progress of the disease timely. The indigenous biocontrol agents that suit local environments may effectively strive with in-situ microorganisms and suppress local pathogen strains. This study aimed to screen antagonistic indigenous compatible Trichoderma and Pseudomonas strains against Fusarium solani. In the pathogenicity test, soil-filled pots were arranged in complete random block design and sown with health faba bean seeds. The effect of some fungicides was evaluated against Fusarium by food poisoning methods to compare with the biocontrol agents . The antagonistic efficacy of biocontrol agents and their compatibility was investigated on Potato dextrose agar medium. Results Fusarium solani AAUF51 strain caused an intense root rotting in faba bean plant. The effect of Mancozeb 80% WP at 300 ppm was comparable with Trichoderma and Pseudomonas strains against Fusarium. The mycelial growth of test the pathogen was significantly ( P  ≤ 0.05) reduced to 86.67 and 85.19% by Trichoderma harzianum AAUW1 and Trichoderma viridae AAUC22 strains in dual culture, respectively. The volatile metabolites of Pseudomonas aeruginosa AAUS31 (77.78%) found the most efficient in reducing mycelial growth of Fusarium followed by Pseudomonas fluorescens AAUPF62 (71.11%) strains. The cell-free culture filtrates of Pseudomonas fluorescens AAUPF62 and Pseudomonas aeruginosa AAUS31 were more efficient than the Trichoderma strain in reducing the growth of Fusarium isolates. There was no zone of inhibition recorded between Trichoderma harzianum AAUW1 , Trichoderma viridae AAUC22 , Pseudomonas aeruginosa AAUS31 , and Pseudomonas fluorescens AAUPF62 strains, hence they were mutually compatible. Conclusions The compatible Trichoderma and Pseudomonas strains showed antagonistic potentiality that could be explored for faba bean protection against black root rot disease and might have a future dual application as biocontrol agents.

Background and aims Planting medicinal herbs under forests is popular as a new cultivation mode for producing high quality herbal medicine. However, soil acidification under forests could aggravate soil-borne diseases, posing a major threat to production. The objective of the study was to investigate strategies for mitigating soil acidification and elucidate its underlying mechanism. Methods We used Panax notoginseng planted under forests with different acidified soil backgrounds to test the effects of exogenous soil amendments on soil chemical properties and rhizosphere microbial communities and then decipher their relationship with root rot disease in P. notoginseng . Results The results indicated that the appropriate dosage of soil amendments with lime, calcium magnesium phosphate, and organic manure individually and their mixture could alleviate root rot disease and promote the growth of P. notoginseng by increasing pH and modifying other soil chemical properties. The abundance and diversity of rhizobacteria increased with increasing soil pH, especially beneficial rhizobacteria including Bradyrhizobium , Rhodoplanes , Mesorhizobium and Gemmatimonas , which modified the soil microbial community by enriching beneficial bacteria and suppressing pathogens to alleviate root rot disease. However, high EC and AN caused by over-dose amendments had the negative impacts on soil microbial communities, resulting in root rot disease exacerbation. Conclusion Alleviating soil acidification to a suitable level could suppress root rot disease by modifying soil chemical properties and enriching beneficial soil rhizobacteria. The findings would be an effective practice toward ameliorating acidic soil under forests to reduce soil-borne disease.