Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling

As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.

Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils

Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.

The occurrence of clubroot in cruciferous crops correlates with the chemical and microbial characteristics of soils

Clubroot disease, caused by Plasmodiophora brassicae, is a serious soil-borne disease in Brassica crops worldwide. It seriously occurs in conducive soils of southern China, while never happens in some areas of northern China with suppressive soils. To understanding the differences, we measured the soil suppressiveness, chemical properties, and microbial communities in suppressive and conducive soils by bioassay and sequencing of 16S and 18S rRNA amplicons. The biological basis of clubroot suppressiveness was supported by the ability to remove it by pasteurization. The pH value and calcium content in the suppressive soils were higher than those in the conducive soils. Suppressive soils were associated with higher fungal diversity and bacterial abundance. The fungal phyla Chytridiomycota, Olpidiomycota, and Mucoromycota and the bacterial phyla Acidobacteriota and Gemmatimonadota were enriched in suppressive soils. More abundant beneficial microbes, including Chaetomium and Lysobacter, were found in the suppressive soils than in the conducive soils. Molecular ecological network analysis revealed that the fungal network of suppressive soils was more complex than that of conducive soils. Our results indicate that plant health is closely related to soil physicochemical and biological properties. This study is of great significance for developing strategies for clubtroot disease prevention and control.

Rhizosphere-associated soil microbiome variability in Verticillium wilt-affected Cotinus coggygria

Introduction

Verticillium wilt is the most devastating soil-borne disease affecting Cotinus coggygria in the progress of urban landscape construction in China.

Methods

To assess the variability of the rhizosphere-associated soil microbiome in response to Verticillium wilt occurrence, we investigated the microbial diversity, taxonomic composition, biomarker species, and co-occurrence network of the rhizosphere-associated soil in Verticillium wilt-affected C. coggygria using Illumina sequencing.

Results

The alpha diversity indices of the rhizosphere bacteria in Verticillium wilt-affected plants showed no significant variability compared with those in healthy plants, except for a moderate increase in the Shannon and Invsimpson indices, while the fungal alpha diversity indices were significantly decreased. The abundance of certain dominant or crucial microbial taxa, such as Arthrobacter, Bacillus, Streptomyces, and Trichoderma, displayed significant variations among different soil samples. The bacterial and fungal community structures exhibited distinct variability, as evidenced by the Bray-Curtis dissimilarity matrices. Co-occurrence networks unveiled intricate interactions within the microbial community of Verticillium wilt-affected C. coggygria, with greater edge numbers and higher network density. The phenomenon was more evident in the fungal community, showing increased positive interaction, which may be associated with the aggravation of Verticillium wilt with the aid of Fusarium. The proportions of bacteria involved in membrane transport and second metabolite biosynthesis functions were significantly enriched in the diseased rhizosphere soil samples.

Discussion

These findings suggested that healthy C. coggygria harbored an obviously higher abundance of beneficial microbial consortia, such as Bacillus, while Verticillium wilt-affected plants may recruit antagonistic members such as Streptomyces in response to Verticillium dahliae infection. This study provides a theoretical basis for understanding the soil micro-ecological mechanism of Verticillium wilt occurrence, which may be helpful in the prevention and control of the disease in C. coggygria from the microbiome perspective.

Microbial diversity in soils suppressive to Fusarium diseases

Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.

Effects of Rhizosphere Microbial Communities on Cucumber Fusarium wilt Disease Suppression

Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the β diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph-ectomycorrhizal-soil saprotroph-wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.

Exogenous melatonin alleviates apple replant disease by regulating rhizosphere soil microbial community structure and nitrogen metabolism

Apple replant disease (ARD) is a common soil-borne disease afflicting apple plants. Melatonin is a broad-spectrum oxygen scavenger that plays a key role in alleviating stress-induced damage in plants. In this study, we aimed to determine whether adding melatonin to replant soil can promote plant growth by improving the rhizosphere soil environment and nitrogen metabolism. In replant soil, chlorophyll synthesis was blocked, reactive oxygen species (ROS) accumulated in large quantities, and membrane lipid peroxidation was aggravated; this eventually resulted in slow plant growth. However, the application of 200 μM exogenous melatonin enhanced the tolerance of plants to ARD by up-regulating the expression of antioxidant enzyme-related genes and increasing ROS scavenging enzyme activity. Exogenous melatonin also increased the absorption and utilization of ¹⁵N by increasing the expression of nitrogen absorption genes and the activity of nitrogen metabolism enzymes. Exogenous melatonin enhanced the soil microbial environment by promoting soil enzyme activity and bacterial richness and decreasing the abundance of several harmful fungi in rhizosphere soil. Mantel test results showed that soil properties (except for AP) and growth indexes were positively correlated with the rate of ¹⁵N absorption and utilization. Spearman correlation analysis showed that the above factors were closely related to the richness and diversity of bacteria and fungi, indicating that the composition of microbial communities might play a key role in mediating change in the soil environment and thus affect nutrient absorption and growth. These findings provide new insights into how melatonin enhances ARD tolerance.

Application of Sophora alopecuroides organic fertilizer changes the rhizosphere microbial community structure of melon plants and increases the fruit sugar content

BACKGROUND

Sophora alopecuroides L. is a leguminous plant commonly found in northwest China. In Xinjiang, the fresh herb of S. alopecuroides is often applied as a green fertilizer to the rhizosphere of melon (Cucumis melo) plants at the end of their flowering period, to improve the taste of the fruits. However, the effects of S. alopecuroides-based fertilizers on the microbial community structure of soil and crop-root systems are unclear. In order to study the sweetening mechanism of the S. alopecuroides organic fertilizer, three different varieties of melon were selected. The untreated plants were used as the control (CK) group, and the plants treated with S. alopecuroides-based organic fertilizer were selected as the treatment (T) group. The physical and chemical properties, enzyme activities and microbial community structure of the rhizosphere samples were also determined, and a correlation analysis with the fruit sweetness index was conducted.

RESULTS

Sugar content of group T was at least 40% higher than that of group CK. The increase in fruit sugar content positively correlated with the increase in the abundance of beneficial microorganisms, including Pseudomonas, Bacillus, Mycobacterium, Burkholderia, Streptomyces, Acinetobacter, Proteobacteria, Lysobacter, Actinomycetes, Penicillium and Aspergillus.

CONCLUSION

Sophora alopecuroides organic fertilizer could alter the composition and function of bacterial and fungal communities and promote the growth of beneficial bacteria in the melon plant rhizosphere. Further, it could increase the content of soluble solids and sugar in the fruits to achieve a sweetening effect. This fertilizer can be applied as a fruit sweetener in melon cultivation, improving the sugar content of the fruit and consequently the sweetness. © 2022 Society of Chemical Industry.

Synergistic Effects of Bacillus amyloliquefaciens SDTB009 and Difenoconazole on Fusarium Wilt of Tomato

Fusarium wilt is a destructive and widespread disease of tomatoes in China, and currently, there are no effective and environmentally friendly control measures. Combining biological control agents with fungicides has become an executable method for disease control. Here, Bacillus amyloliquefaciens SDTB009 showed excellent in vitro antagonistic activity against Fusarium oxysporum and tolerance to high concentrations of difenoconazole (200 mg/liter) in vitro. The combination of SDTB009 and difenoconazole exhibited more effectiveness in mycelial growth inhibition than either treatment alone. Compared with that in the SDTB009 bulk solution in vitro (5.22 g/liter), surfactin titer reached 7.15 g/liter in the 100 mg/liter of difenoconazole-containing medium. Interestingly, the upregulation of 20 genes in the surfactin biosynthesis pathway from 2-fold to 4-fold was observed, explaining the synergistic effect. The SDTB009 combined with varying concentrations of difenoconazole (60, 120, and 150 g a.i./ha) showed a synergistic effect in two consecutive years of field trials. These results show that the integration of difenoconazole with the biocontrol agent B. amyloliquefaciens SDTB009 synergistically increases the control efficacy of the fungicide against tomato Fusarium wilt.

Impact of biocontrol microbes on soil microbial diversity in ginger (Zingiber officinale Roscoe)

BACKGROUND

Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) that directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.

RESULTS

MiSeq sequencing of the 16S rRNA gene was used to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentrations. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.

CONCLUSION

The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should be noticed in plant disease management. © 2021 Society of Chemical Industry.

The fungal community outperforms the bacterial community in predicting plant health status

Characterizing the relationship between soil biotic and abiotic properties and plant health status is crucial to understanding the pathogenesis of soil-borne diseases. Here, we compared these properties in the soils of lisianthus with different disease incidence plots and report the cause-effect relationship between soil properties and plant health status using heat treatment coupled with microbiota self/across re-inoculations. The relative importance of soil bacterial and fungal communities in predicting plant health was also analyzed. Results showed that the soils with low and high disease incidences (LDS and HDS) harbored differential microbial communities and physicochemical properties. The LDS soil had relatively low Fusarium oxysporum abundance, electrical conductivity (EC), and NO₃^--N content. Soil microbial community was the direct determinant of plant health. The disease-suppressive activity of the microbiome in the LDS soil could be transferred to the HDS soil. Also, the relative importance of the fungal community in predicting plant health status was greater than that of the bacterial community, as reflected by (1) the fungal community could drive more complex networks related to healthy plants and (2) the diversity and core taxa of the fungal community had higher mean predictor importance values for plant health. The relative abundances of core genera Acremonium, Mycothermus, and Chryseolinea were significantly and negatively correlated with the disease incidence and the abundances of pathogens, identifying these genera as potential disease-suppressive agents. Taken together, our results reveal a direct relationship between soil properties and plant health status, in which the fungal community composition is most important for predicting plant health status. KEY POINTS: • Soil with differing pathological groups harbors distinct microbial communities. • Soil microbial communities directly determine the plant's health status. • Fungal community is a better predictor of plant health than the bacterial community.

Palmitic acid mediated change of rhizosphere and alleviation of Fusarium wilt disease in watermelon

Palmitic acid (PA) in root exudates or decaying residues can reduce the incidence of soil-borne diseases and promote the growth of some crop plants. However, the effects of PA on soil-borne pathogens and microbial communities are poorly understood. Here, we investigate the effects of PA on overall watermelon microbial communities and the populations of Fusarium oxysporum f.sp. niveum (Fon). The effects of PA on the mycelial growth and spore production of Fon were tested in vitro, while its effects on Fon, total bacteria and total fungi populations, and microbial communities were evaluated in a pot experiment. The results revealed that all test concentrations of PA inhibited Fon mycelia growth and spore production. The pot experiment showed that 0.5 mM and 1 mM PA reduced Fon but increased total bacteria populations, and 0.5 mM and 1 mM PA 0.5 mM and 1 mM PA promoted the change to a soil type of bacteria soil. Meanwhile, 0.5 mM PA and 1 mM PA altered the community composition of the rhizosphere microorganisms and reduced the relative abundance of two bacterial operational taxonomic units (OTUs) and the two fungal OTUs that were significantly (p < 0.01) related with disease severity and increased that of four bacterial OTUs and the two fungal that were highly significantly (p < 0.01) negatively correlated with the disease severity. These results suggest that application of PA decreased the populations of Fon, changed the rhizosphere microbial composition, reduced the disease severity of Fusarium wilt, and promoted the growth of watermelon.

Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing

Root rot reduces the yield and medical quality of C. chinensis (Cc). Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. The present study aimed to identify potential pathogenic and antagonistic microorganisms associated with root rot based on a high-throughput sequencing technique to prevent this disease. Healthy and diseased Cc in the endosphere and rhizosphere from the same field were collected to investigate the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The numbers of animal pathogens, soil saprotrophs, plant saprotrophs, and wood saprotrophs in the endosphere of diseased Cc were higher than those in the healthy endosphere and were dominated by Phaeosphaeriaceae, Cladorrhinum, Fusarium, Exophiala, and Melanommataceae. Fusarium, Volutella, Cladorrhinum, Cylindrocarpon, and Exophiala were significantly enriched in the endosphere of the diseased plants. Co-occurrence network analysis showed that Bacillus was negatively correlated with Fusarium, Volutella, and Cylindrocarpon, indicating that Bacillus may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum were isolated and verified as pathogens, and 14 Bacillus strains were isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached roots. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results provide research ideas and microbial resources for future studies on mitigating or preventing root rot damage to Cc.

Pathogen Infection and Host-Resistance Interactively Affect Root-Associated Fungal Communities in Watermelon

Interactions of pathogen infection, host plant resistance, and fungal communities are poorly understood. Although the use of resistant watermelon cultivars is an effective control measure of watermelon wilt disease, fungal communities may also have significant effects on the development of the soil-borne pathogen complexes. We characterized the root and rhizosphere fungal communities associated with healthy and diseased watermelons of three different cultivars with different susceptibilities toward wilt disease by paired-end Illumina MiSeq sequencing. Thirty watermelon plants including highly wilt-resistant, moderately resistant, and susceptible cultivars were collected from a greenhouse, half of which showing clear wilt symptoms and the other half with no symptoms. Patterns of watermelon wilt disease and the response of the fungal communities varied among the three cultivars. The amount of the pathogen Fusarium oxysporum f. sp. niveum was higher in diseased root and rhizosphere samples, particularly in the susceptible cultivar, and was significantly positively correlated with the disease index of Fusarium wilt. Plant health had significant effects on root-associated fungal communities, whereas only the highly resistant cultivar had significant effects only on the rhizosphere fungal communities. Co-occurrence networks revealed a higher complexity of fungal communities in the symptom-free roots compared to diseased roots. In addition, networks from roots of the highly resistant plants showing symptoms had a higher complexity compared to the susceptible cultivars. Keystone species were identified for the plants with different symptom severity and the different cultivars in the root and rhizosphere, such as Fusarium oxysporum, Monosporascus cannonballus, and Mortierella alpina. Overall, the most important factor determining fungal communities in the roots was plant symptom severity, whereas in the rhizosphere, plant genotype was the most important factor determining fungal communities.

Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils

The different impacts, especially on soil physicochemical and microbial characteristics, among disinfestation methods based on different principles (including physical, chemical, and biological) have not been illustrated well. Here, we used steam sterilization, dazomet fumigation, and reductive soil disinfestation (RSD) methods representative of physical, chemical, and biological soil disinfestation, respectively, to disinfest seriously degraded greenhouse soils before watermelon cultivation in one season. Compared with the control, RSD significantly decreased the soil nitrate content by 85.9% and the electrical conductivity by 52.0% and increased the soil pH to 7.44. Although all three soil disinfestations significantly decreased the abundance of the pathogen Fusarium oxysporum by 83.0-99.2%, their impacts on soil microbial characteristics were variable. Briefly, steam sterilization significantly changed multiple bacterial and fungal properties. Dazomet fumigation impacted mainly fungal properties, such as abundance, diversity, and community structure, but RSD significantly decreased bacterial diversity and altered the bacterial community structure. Although the differences mentioned above got smaller after watermelon cultivation, the plant performances differed dramatically in different soils. The largest plant biomass, fruit ratio, and yield were found in the RSD-treated soil, whereas the lowest fruit ratio and yield were found in the steam-sterilized soil. The soil nitrate content, electrical conductivity, bacterial diversity and community structure, and some specific microbial agents, such as Aspergillus, Cladosporium, and Pseudomonas, were correlated with plant performance. RSD is a promising soil disinfestation strategy to support plant growth in intensively cultivated greenhouse soils with serious problems, such as acidification, salinization, and pathogen accumulation.