Dazomet application suppressed watermelon wilt by the altered soil microbial community

Watermelon (Citrullus lanatus) is highly susceptible to Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (FON), leading to severe yield and quality losses. Management options include grafting, chemical and biological control, and resistant cultivars. Dazomet is a soil fumigant used against soilborne pathogens, pests, and weeds, and previous lab and field studies have shown efficacy in various crops. Concurrently, research has highlighted that plant immune systems shape root and soil microbiomes, which in turn can enhance plant immunity and disease suppression. However, how soil microbes change in watermelon soils defending against Fusarium wilt after dazomet application remained unclear. Based on prior work indicating that soil microbial community structure plays a key role in plant growth and disease occurrence, the authors hypothesized that changes in soil environmental factors and/or microbial community constructors after dazomet application in continuous watermelon-cropping soil could affect plant immune defenses against Fusarium wilt. The study therefore examined soil microbial diversity at six time points across two seasons following dazomet application using Illumina MiSeq to track dynamic community changes and their role in disease suppression.

The paper reviews reports that dazomet fumigation can control soilborne diseases across crops: efficacy in integrated management of ginger bacterial wilt in China; modification of beneficial soil microbiota in apple orchards with replant disease; and improvements in soil metabolic activity and functional diversity by reductive soil disinfestation-related treatments. It summarizes evidence that plant immune systems shape microbiomes and that microbiomes can enhance plant immunity, with interkingdom microbe-microbe interactions in roots influencing plant survival. Prior studies showed that manipulating soil microbial ecological balance can suppress crop diseases and that fertilization regimes alter soil microbial communities and watermelon Fusarium wilt incidence. The review also notes specific beneficial microbes: Bacillus and Paenibacillus produce antimicrobial polyketides and lipopeptides; Pseudomonas can directly reduce virulence of pathogenic fungi; Nitrospira and Nitrolancea are involved in nitrogen cycling; and Penicillium spp. (e.g., P. oxalicum) can control F. oxysporum in cucurbits. It also highlights literature linking phosphorus availability, root microbiota, and plant immunity, suggesting nutrient-microbiome-immunity integration.

Site and design: Field experiments were conducted at Gaoqiao Scientific Research Base, Hunan Academy of Agricultural Sciences, Changsha, Hunan, China (112°58′42″ E, 28°11′49″ N) in 2018 and 2019 on sandy loam soil. Watermelon cultivar Zaojia 8424 was used. Six greenhouses (30 m × 6 m), each under five years of watermelon monocropping, were selected; three received dazomet (DAZ) and three served as controls (CK). Routine cultivation was identical across greenhouses. Dazomet application: Each March before transplanting, 6 kg of 98% dazomet (C3H8N2S2) per greenhouse was applied and incorporated by rotary tillage to 0–20 cm for uniform mixing. When soil temperature exceeded 8 °C, film mulching retained fumigant and moisture (~40%). After 20 days, film was removed and greenhouses ventilated. Fifteen days later, nursery-grown seedlings were transplanted at 50–60 cm spacing. Sampling scheme: Six sampling times were established: (1) Mar 6, 2018 (pre-dazomet), (2) Apr 24, 2018 (seedling stage), (3) May 3, 2018 (wilt symptom appearance), (4) Mar 6, 2019 (pre-dazomet), (5) Apr 22, 2019 (seedling), (6) Apr 29, 2019 (wilt symptom appearance). For each greenhouse, nine 0–20 cm soil cores in an S-pattern were pooled per replicate; three greenhouses per treatment served as biological replicates. Total samples: 36. Disease assessment: Fusarium wilt incidence (%) = infected plants/total surveyed × 100, monitored throughout onset (from root rot/vascular browning to plant death). Soil physicochemical properties: pH (1:2.5 soil:water), electrical conductivity via conductivity meter from 5:1 water extracts, soil organic matter by dichromate oxidation, total and available P and K by ICP-AES after acid digestion, total N (Kjeldahl) and available N (alkali diffusion). Details in Supplementary Table S1. DNA extraction and amplicon sequencing: Total soil DNA extracted with E.Z.N.A Soil DNA kit; quality checked by Nanodrop and agarose electrophoresis. 16S rRNA V3–V4 amplified with 338F/806R; fungal ITS1 with ITS1F/ITS2R. PCR conditions: 95 °C denaturation, 27 cycles for ITS or 35 cycles for 16S with 55 °C annealing and 72 °C extension, final extension 72 °C 10 min. Amplicons purified (AxyPrep), quantified (QuantiFluor-ST), pooled equimolarly and sequenced (Illumina MiSeq, 2×300 bp) by Majorbio (Shanghai). Reads deposited in NCBI SRA: SRP268536. Quantitative PCR for FON: Specific primers were used for FON detection. Conventional PCR generated a 1446 bp fragment containing the qPCR target to construct a standard curve. qPCR performed on Bio-Rad iQ5 with specified cycling conditions; melting curves obtained from 65–95 °C in 0.5 °C increments. Bioinformatics and statistics: FASTQ reads demultiplexed, quality-filtered with Trimmomatic (sliding window Q<20 trimmed; reads <50 bp discarded), merged with FLASH (overlap >10 bp), with exact barcode/primer matching and removal of ambiguous bases; singletons removed. OTUs clustered at 97% similarity using UPARSE v7.1; chimeras removed with UCHIME. Taxonomy assigned by RDP Classifier against SILVA SSU123 (16S) and UNITE 8.0 (ITS) at 70% confidence. Diversity analyses performed using QIIME2 on Majorbio Cloud: rarefaction (sobs), alpha diversity (Shannon, Student’s t-test), beta diversity (NMDS with ANOSIM). Differential abundance tested by Kruskal–Wallis H tests at OTU/phylum/genus levels; multiple testing corrections via FDR and Tukey’s method. One-way ANOVA and Student’s t-tests used for group comparisons. Correlations between environmental factors (e.g., available P) and taxa assessed via Spearman correlation heatmaps (MeV). Additional statistics with SPSS 20. Figures prepared using Microsoft Office 2010 and Adobe Illustrator CS5.

• Disease suppression: Dazomet significantly reduced watermelon Fusarium wilt incidence compared to control across both years. Control morbidity exceeded 98% in 2018 and 2019. In DAZ-treated plots, disease incidence decreased markedly, with 2018 at 79.82% and 2019 at 34.17% (lower in 2019 than 2018).
• Soil properties: Among measured parameters, EC and available phosphorus (AP) differed; EC was lower in 2019 than 2018 in DAZ soils, and AP increased significantly after dazomet application.
• Bacterial sequencing metrics: 36 samples yielded 2,062,735 raw reads, 1,491,552 clean reads, averaging 41,432 reads/sample; 8,599 OTUs detected. Rarefaction indicated adequate depth. Alpha diversity (Shannon) differed significantly between DAZ and CK; NMDS showed compositional dynamics across times and treatments. Venn diagram showed 850 shared bacterial OTUs across groups. Several core OTUs changed significantly; e.g., Nitrolancea-associated OTU accumulated in DAZ at most time points; Arthrobacter increased at times 2 and 4; Pseudomonas increased at times 4 and 5; Pullulanibacillus increased at time 4.
• Dominant bacterial taxa shifts: Phyla Cyanobacteria, Nitrospirae, and FCPU426 changed significantly with DAZ; Nitrospirae decreased in 2019 and at time 5 versus CK. At genus level, significant dynamics observed for Acidipila, Aquicella, Bacillus, Nitrolancea, Nitrospira, Paenibacillus, Pseudomonas, and Streptomyces. Notably, Pseudomonas and Nitrolancea increased after DAZ, while Aquicella and Nitrospira decreased (especially in 2019).
• Fungal sequencing metrics: 1,318,001 raw reads, 939,816 clean reads, averaging 26,106 reads/sample; 1,832 OTUs detected. Alpha diversity (Shannon) differed between treatments; NMDS indicated dynamic community shifts. Venn diagram showed 50 shared fungal OTUs. Core OTUs included Penicillium (Aspergillaceae; Eurotiales), which increased significantly in 2019 compared to 2018.
• Dominant fungal taxa shifts: Phyla Ascomycota and Mortierellomycota changed significantly after DAZ, in opposite directions. Genera Chaetomium, Fusarium, Mortierella, and Penicillium altered significantly; Penicillium increased rapidly after DAZ, while Mortierella and Fusarium decreased versus CK.
• Pathogen quantification: qPCR showed FON levels consistently decreased after DAZ; in 2019, FON content was significantly lower in DAZ than CK.
• Correlations: Beneficial microbes (Paenibacillus, Bacillus, Nitrolancea, Penicillium) correlated positively with AP and negatively with disease incidence. RDA and Spearman analyses supported associations between increased AP, enrichment of beneficial taxa, and reduced morbidity.

The study demonstrates that dazomet application not only suppresses Fusarium wilt in watermelon but also reshapes the soil microbiome. Significant alterations in both bacterial and fungal communities were detected in DAZ-treated soils across two seasons, with enrichment of taxa known for plant-beneficial functions (e.g., Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Penicillium) and reduction of Fusarium and FON. These beneficial taxa are associated with antimicrobial metabolite production, nutrient cycling (e.g., nitrification), and plant immunity enhancement, offering plausible mechanisms for disease suppression. Increased available phosphorus (AP) after DAZ was strongly and positively correlated with several beneficial taxa and negatively with disease incidence, suggesting an interplay between nutrient availability, microbiome assembly, and plant immune responses. This aligns with prior findings that plant immunity shapes microbiota and that root microbiota integrate phosphate stress signaling with defense. The cumulative evidence indicates that DAZ-mediated changes in soil chemistry (notably AP) and biota favor a microbiome that supports plant health and suppresses pathogens, contributing to the observed reduction in wilt incidence, particularly more pronounced in the second year.

Dazomet application significantly suppresses watermelon Fusarium wilt, concomitant with pronounced shifts in soil microbial community structure. Beneficial microbial genera (e.g., Bacillus, Paenibacillus, Pseudomonas, Nitrolancea, Penicillium) were enriched, whereas Fusarium and FON declined. Available phosphorus increased after DAZ and correlated positively with beneficial microbes and negatively with disease incidence. Two non-exclusive mechanisms are proposed: (1) increased AP stimulates plant immune functions that recruit beneficial microbes, establishing a protective community; (2) DAZ-induced AP changes directly favor specific microbes that contribute to pathogen suppression. These findings motivate future research to dissect microbiota–plant immunity interactions and nutrient-mediated assembly processes to optimize disease management strategies.