Responses of Soil Microbial Communities to the Invasion of Fusarium Oxysporum and Screening for Fusarium Antagonistic Microorganisms From Pathogenic Soil

Fusarium oxysporum is known as a biological pollutant in the farmland soil, that causes vascular wilt on a wide range of cash crops, which is the most destructive disease of plant worldwide. F. oxysporum is a fungus that can colonize and grow saprophytically in plant debris and increase pathogen viability in soil. It is almost impossible to remove once successful colonization. How to effectively reduce the pathogen population and restore the benecial microbial community in soil is an important subject to control the Fusarium wilt. The main objective of this study is to explore inuences of F. oxysporum invasion on the microbial community and to screen ecient biocontrol agents from microorganisms with changing relative abundance. Results In this study, we evaluated that responses of the soil microbial communities to invasion of F. oxysporum. We found that F. oxysporum invasion could modify soil physical-chemical properties, soil enzymes activities, microbial community structure and diversity of the soil microbes. We screened and identied an ecient biocontrol strain, Talaromyces purpurogenus Q2, which could be used for defense and suppression of F. oxysporum in bitter gourd and eciently decreasing incidence of the Fusarium wilt of bitter gourd in the greenhouse and in the eld. The research results of biocontrol mechanisms showed that T. purpureogenus strain Q2 involved in the resistance of soil microbial communities to invasion of F. oxysporum, and the density of F. oxysporum was inhibited by exogenous T. purpureogenus and the resident microbes that strain Q2 promoted their growth. In the co-culture of strain Q2 and F. oxysporum, we further observed that T. purpurogenus Q2 could signicantly suppress the mycelia growth and development of F. oxysporum by secreting cell wall degrading enzymes, and hinder cell wall formation by suppressing the gene expression of cell wall biosynthesis, such as FomCFEM that is essential for full virulence and stress tolerance in F. oxysporum. agents from microorganisms with resistance to the invasion of F. oxysporum. The mechanisms of Talaromyces purpurogenus strain Q2 protected bitter gourd from F. oxysporum is to reduce the relative abundance of rhizospheric F. oxysporum by inhibiting the growth and development of F. oxysporum. This work can provide a new biocontrol agent for biocontrol of Fusarium wilt and soil-born diseases of other horticultural crops. microbial communities to the invasion of F. oxysporum and screened out a new Talaromyces sp. with biological control potential, and investigated the control ecacy and control mechanism of the Talaromyces sp. on the Fusarium wilt. Furthermore, the effects of Talaromyces sp. on the metabolic pathways and related gene expression of F. oxysporum during interactions between Talaromyces sp. and F. oxysporum were studied and described, and the effects of these genes on the growth, development, and pathogenicity of F. oxysporum were claried. (Control), inoculation (S-FOM), pathogenic antagonistic (TP). of gourd (2 part of the soil for isolation and screening of benecial microorganisms, a part of the soil for DNA stored -80 and the rest soil for soil fertility stored at 4 The soil physicochemical the the soil activities changes of ability enzyme Activity Determination enzyme Activity have been described the S2. sequenced genome novo sequencing Pacbio microbial species Actinobacteria, 6.52% microbial species belong Firmicutes, 3.78% to Thaumarchaeota, 3.08% microbial species belong to Euryarchaeota, and 2.91% microbial species belong to Ascomycota (Supplementary Fig. S8C). The relative abundance of Actinobacteria and Firmicutes were higher in TP treatment than in Control and S-FOM. among the of 20 nodes, sunch as and module The The microbe, (36.36%), Actinobacteria (25.17%), Firmicutes (5.59%), Euryarchaeota (2.94%), Thaumarchaeota (2.94%), Bacteroidetes (1.82%), and Ascomycota (1.68%). The results suggest that Proteobacteria and Actinobacteria in soil were more often located in core positions in the network than other species. belonging to biological process (BP), molecular functions (MF) and cellular component (CC) categories. In the all category, the highly represented groups were ‘intrinsic component of membrane’ (410 up-regulated genes and 748 down-regulated genes), ‘integral component of membrane’ (410 up-regulated genes and 744 down-regulated genes), ‘membrane part’ (416 up-regulated genes and 748 down-regulated genes), ‘membrane’ (428 up-regulated genes and 762 down-regulated genes), ‘oxidoreductase activity’ (355 up-regulated genes and 207 down-regulated genes), ‘transmembrane transport’ (149 up-regulated genes and 256 down-regulated genes) and ‘transmembrane transporter activity’ (65 up-regulated genes and 146 down-regulated genes) groups. In the Q2-FOM groups, the genes associated with membrane and transport appeared to be the most signicantly enriched. To further investigate the biochemical pathways of these DEGs in the process of T. purpureogenus inhibiting the growth of Fom, we mapped all DEGs identied in the RNA sequencing to terms in the KEGG database. The results showed the DEGs could be classied into four pathways, including metabolism, genetic information processing, environmental information processing and cellular processes. Top 20 enriched KEGG pathways associated with DEGs affected by T. purpureogenus were showed in Supplementary Fig. S11B, including glyoxylate and dicarboxylate metabolism, glutathione metabolism, valine, leucine and isoleucine degradation, glycerophospholipid metabolism, phenylalanine metabolism, nitrogen metabolism, propanoate metabolism, pyruvate metabolism, ABC transporters, galactose metabolism, tyrosine metabolism and glycerolipid metabolism. These results further indicated that stress of strain Q2 may greatly inuence carbohydrate metabolism, amino acid metabolism, lipid metabolism, energy metabolism, component of membrane and membrane transport of F. oxysporum. assays (0.7 mol·L − 1 NaCl and 0.7 mol·L − 1 KCl), osmotic (1 mol·L − 1 sorbitol), H 2 O 2 (5 mmol·L − 1 and cell wall stress (0.05% SDS, and 0.2 g·mL − 1 CR) respectively. The results showed that the ∆ hypersensitive the cell wall stress compared with WT and ∆ FomCFEM-C strain These results indicated that ∆ important role in the integrity and function of the cell wall of F. oxysporum f. momordicae. changed indigenous microorganisms, unknown that the role the tendency may reached the stage of eld trials [39]. But most biocontrol fungi are still in the theoretical or conceptual stage owing to several factors including stability in eld and diculty in solid fermentation. Obtaining these biocontrol fungi with stable biocontrol effect and easy fermentation are the main factor for their successful application. In our study, we obtained 14 biocontrol agents with strong antagonistic activity to F. oxysporum on plate, originally separated from the pathogenic soil of Fusarium wilt. In the comprehensive evaluation of the 14 biocontrol agents, we found T. purpureogenus strain Q2 had more stable and constant biocontrol ecacy on Fusarium wilt than Trichoderma and Bacillus in the greenhouse and eld and the strain Q2 could stably colonize in the soil. Meanwhile, the strain Q2 showed the biocontrol potential against various pathogenic fungi, especially F. oxysporum. However, the biocontrol strains (bacteria or fungi) with an antagonistic effect on pathogen propagule initiate sustained disease suppression after reaching threshold population sizes (10 5 cfu/g) [40]. In our study, the Fusarium wilt still occurred, although the relative abundance of strain Q2 increased in the process of F. oxysporum invading the soil, this does not prove that the total microbiome including strain Q2 did not contribute to reduce the incidence of Fusarium wilt. The strain Q2 reached the threshold of population sizes (1×10 6 cfu/g) by human intervention and started continuous disease suppression through inhibiting the growth and development of F. oxysporum. This has also been observed during the co-culture of strain Q2 and F. oxysporum f. sp. momordicae. Meanwhile, the strain Q2 can also excite the activity of other benecial microorganisms such as actinomycetes. These results show that strain Q2 directly or indirectly suppresses the growth of F. oxysporum in the soil, and strain Q2 may be just the key player, other microbes play a supporting role. showed that growth of Fom was signicantly inhibited in the presence of strain Q2. In addition, β-1, 3-glucanase and chitinase enzymes production was improved in a combination inoculated with strain Q2 and Fom. Similarly, Copete-Pertuz identied a triple combination inoculated with Trichoderma viride and Aspergillus sterreus into a 7th day pre-culture of Leptosphaerulina sp. improved ligninolytic enzymes production when compared to the Leptosphaerulina sp. monoculture [49]. Meanwhile, our results showed that the content of malondialdehyde (MDA) and chitin of F. oxysporum mycelia had changed under the presence of strain Q2. This indicated that the change of the membrane permeability and cell wall structure of F. oxysporum hypae, and the damage degree of membrane system and cell wall was increased with the increase of strain Q2 density. The study on transcriptomes also brought useful information on the interaction between strain Q2 and Fom. RNA-seq data indicated that F. oxysporum membrane components, as well as transmembrane transport, seemed to have been seriously affected by the strain Q2 at the transcriptome level. The inhibitions observed on both growth and membrane function of Fom in our study were in accordance with those of Strub [50]. The membrane components and transmembrane transporter of F. verticillioides were affected by Streptomyces sp. AV05 during their co-cultivation [50]. T. purpureogenus strain Q2 was a soil and rhizosphere microorganisms, isolated from the rhizosphere of healthy plant planted in the pathogenic soil of F.oxysporum. In the present study, strain Q2 has antagonistic activity against a variety of pathogens, especially against F. oxysporum and has a good control effect on Fusarium wilt of bitter gourd. Our results indicated that the mechanisms of strains Q2 protected bitter gourd was to reduce the relative abundance of rhizospheric F.oxysporum by direct and indirect inhibiting the growth and development of F. oxysporum, because the positive correlations were found between wilt. new study demonstrates that we have screened a ecient biocontrol agents, Talaromyces purpurogenus strain Q2, from microorganisms with resistance to the invasion of F. oxysporum. The biocontrol mechanisms of T. purpurogenus strain Q2 protected bitter gourd from F. oxysporum is to reduce the relative abundance of rhizospheric F. oxysporum by inhibiting the growth and development of F. oxysporum. This work can provide a new biocontrol agent for biocontrol of Fusarium wilt and soil-born diseases of other horticultural crops.


Study sites and soil sample collection
We collected soil samples (the standing plant was bitter gourd) at a long-term experimental station of the Shandong Agricultural University, in Taian of Shandong Province, China, August to November 2019. The arti cial disease nursery of Fusarium wilt was established in the experimental station in 2015 to investigate the disastrous mechanisms and control strategies of exogenetic invasive F. oxysporum. The incidence of Fusarium wilt of bitter gourd is 100% from 2017 to 2019. Three treatments with ve replicates were set up, including healthy soil without Fusarium inoculation (Control), pathogenic soil with Fusarium inoculation (S-FOM), and the pathogenic soil with Fusarium inoculation was treated with antagonistic fungus (TP). We collected 1 kg soil samples from the rhizosphere of bitter gourd in each plot. The collected soil samples were sieved (2 mm). A part of the soil for isolation and screening of bene cial microorganisms, a part of the soil for DNA extraction was stored at -80 ℃, and the rest soil for soil fertility was stored at 4 ℃. The soil physicochemical characterizations were measured based on the norm system, the soil enzyme activities (i.e. soil uorescein diacetate hydrolase, soil urease, soil polyphenol oxidase and soil acid phosphatase) were measured according to instructions of the kit (Beijing Solarbio Science & Technology Co., Ltd.).

Isolation of biocontrol agent from the pathogenic soil
Approximately 10 g soil was incubated in 100 mL of sterile distilled water and constantly shaked at 200 rpm for 30 min. 0.2 mL diluted soil extract was plated on PDA medium Petri plates. Plates were then incubated at 28℃ for 3-5 days and the growing colonies were transferred to new Petri dishes with PDA medium in order to establish bacterial or fungal pure cultures. More than 100 colonies were collected and used in subsequent screenings. All microbial collections isolated from the pathogenic soil were tested for antagonism against Fom. Antagonistic examination of microbial isolates against Fom was performed in vitro using PDA plates. Agar disks of Fom was applied on the Petri dish 6 cm apart from each microbial culture spot. The Petri dishes were then incubated at 28℃ for 7 days. The percentage of mycelia growth inhibition I (%) by isolated strain was calculated according to the following formula: I (%) = (1 − Dn/Do) × 100, where I (%) represents the mean inhibition of mycelia growth, Dn represent the mean diameter of fungal pathogens growth in the presence of isolated strain, and Do represents the mean diameter of fungal pathogens growth in the absence of isolated strain (Control). 14 microbial isolates showing high Fom inhibition were named SK1-SK6, KG-1, Q1-Q2, and M1-M5 (Supplementary Table S1).

Morphological and molecular identi cation of Talaromyces sp. strain Q2
Talaromyces sp. strain Q2 was inoculated and grown on Petri dishes (90 mm) with potato dextrose agar (PDA) medium at 25°C in the dark, which were performed in triplicate. 2-5 days later, the morphology observation of conidiophores and conidia was performed under Nikon Eclipse 90i microscope (Nikon, Tokyo, Japan). The pure strains were incubated on different media including Czapek agar (CA), Czapek yeast extract agar (CYA), Sabouraud maltose agar (SMA), Corn meat agar (CMA), Martin media (MM), Sabouraud sucrose agar (SSA), Sabouraud dextrose agar (SDA), Oatmeal agar (OA) at 25°C for 7 days, and the colony morphology and microscopic characters were examined, measured and photographed. Morphological identi cation of Talaromyces sp. strain Q2 was conducted according to the references of Visagie and Su [19,20]. β-1, 3-glucanase and chitinase produced by strains Q2 were determined qualitatively by the clear zone method on β-D-glucan and colloidal chitins-containing agar plate. At the same time, we also tested the changes of the enzyme-producing ability of strain Q2 induced by the different substrate. The β-1, 3-glucanase and chitinase were assessed quantitatively by chitinase enzyme Activity Determination Kit and β-1, 3-glucanase enzyme Activity Determination Kit (Beijing Solarbio Biotechnology Co., Ltd.), respectively.
Fungal mycelium was harvested from the surface of PDA medium and frozen by liquid nitrogen. Then the DNA samples of strain Q2 were extracted using the Fungal Genomic DNA Kit (BioTeKe Biotech Co. Ltd, Beijing, China) according to the manufacturer's instructions and stores at -20˚C. Primers of ITS1/ITS4, Bt2a/Bt2b, and cmdAD1/cmdQ1 were used to identify the strain Q2 [21,22,23]. The primers, PCR program, and the reference sequence used in the current study have been described in the Supplementary Table S2. The genomes of strain Q2 was sequenced using the whole genome de novo sequencing at the Illumina NovSeq platform and Pacbio Sequel platform.

The solid fermentation of strain Q2
On the basis of our previous research, we selected wheat grain, corn straw, and humic acid as the main material of solid fermentation medium. Orthogonal test table L 9 (3 4 ) was used for studying the optimal solid-state fermentation media formula of strain Q2. The optimal solid-state fermentation media formula of strain Q2 was 66.67% wheat grain, 14.29% corn straw, 19.05% humic acid, and 65.0% moisture and the number of spores can reach 6 ×10 9 cfu·g − 1 (Supplementary Table S3). After drying, culture material was crushed and adjusted spores concentration containing 2×10 7 cfu·g − 1 .

Antagonism assay in vitro and in vivo
The ability of strain Q2 to inhibit the growth of pathogenic fungi listed in Sect. 2.1 has been investigated. Antagonism of strain Q2 against pathogenic fungi was conducted in vitro using PDA plates as described in Sect. 2.3.
For the study on the control e cacy of strain Q2 in greenhouse and eld, healthy bitter gourd seedlings with 2-4 leaves were selected and transplanted to health soil and pathogenic soil containing fungal pathogen inocula of Fusarium wilt, the preparation of soil infested with the pathogenic fungus was conducted according to Wang [24]. 15 g of microbial agents of strain Q2 were poured for each plant in health soil (H-TP) and pathogenic soil (TP). And the equal amounts of solid fermentation medium without strain Q2 was poured for each plant health soil (Control) and pathogenic soil (S-FOM), all the seedlings were cultured at the same condition. After transplantation for 30 days, diseased incidence and disease index of bitter gourd seedlings were investigated.
Control e cacy of Fusarium wilt of bitter gourd was calculated. Six classes were divided according to Chen [25]. The density of Fusarium spp. in the bitter gourd rhizosphere was estimated by metagenomic sequencing and dilution plating (using Fusarium selective medium Komada's medium [26].

2.7
The mechanism of strain Q2 inhibiting the growth of FOM In order to verify the mechanism of strain Q2 inhibiting the growth of Fom. Two treatments with three replicates were set up, including the sample singlycultured of Fom (Control treatment) and the sample co-cultured with strain Q2 and Fom (T). Spores of strain Q2 and Fom were washed with sterile water, the nal concentration of 4×10 7 cfu·ml − 1 and 2.5×10 7 cfu·ml − 1 , respectively. Subsequently, 0.8 mL of conidial suspensions of Fom combined with 0 ml (Control), 0.05 ml (T1), 0.5 ml (T2), 1.0 ml (T3), 2.5 ml (T4), and 5.0 ml (T5) of conidial suspensions of Q2 in multiple proportions were inoculated into 100 mL PDB, cocultured at 180 rpm·min − 1 and 28°C for 3-5 days. The growth of Fom in different treatments was recorded by measuring the spore number of Fom. The axenic culture was ltered through three layers of gauze, and then ltrates were centrifuged at 8000 rpm·min − 1 for 10 min, and supernatant was discarded. Spores were precipitated and then were used to analyze the effects of strain Q2 on the metabolic activity of Fom (i.e. N-acetylglucosamine content of fermentation supernatant liquid, intracellular glycerol content and malondialdehyde content, they were measured according to instructions of the ELISA kit (Jiangsu Jingmei Bioechnology Co., Ltd.)). Meanwhile, we had chosen the sample singly-cultured of Fom (Control treatment) and the sample co-cultured with strain Q2 and Fom (T3 treatment group) for transcriptome sequencing, there were named FOM and Q2-FOM, respectively.
2.8 Identi cation of the role of a CFEM domain-containing protein orthologue gene from Fom Generation of FomCFEM deletion mutants FomCFEM deletion mutants were generated by the split-marker approach. Brie y, a 760-bp upstream sequence and a 1027-bp downstream sequence fanking the FomCFEM gene were ampli ed with primer pairs CFEM-AF/R and CFEM-BF/R, respectively. The hygromycin phosphotransferase (hph) gene was ampli ed from pCB1003 plasmid with primer pairs HYG-F/HY-R and YG-F/HYG-R. Two equal quantities of the fragments (a total of 20 µg) were transformed into protoplasts of Fom, and the resulting transformants selected on TB3 medium containing 100 µg/mL hygromycin B were identi ed by polymerase chain reaction (PCR) with primers (CFEM-F/R, CFEM-K1F/R, and CFEM-K2F/R) and southern blot analysis. For southern blot assay, genomic DNA was extracted from mycelia of each strain as described previouslyand digested with Pvu I [27,28]. The DNA probe was ampli ed by PCR using the primer pairs tCFEM-F/R. Southern blot analysis was performed with a DIG High Prime DNA Labeling and Detection Starter kit I (Roche Diagnostics, Mannheim, Germany) according to the manufacturer's protocol. According to the size difference between the wild-type and ΔFomCFEM strain hybrid fragments, the correctness of the converter was judged. The primer sequences for each gene product are listed in Supplementary Table S4. Complementation of FomCFEM For complementation assays, a 2.6-kb fragment bearing 1.1 kb of the full-length FomCFEM gene and 1.5 kb of its promoter was ampli ed with the primer pair Ech1-CF/Rand then cloned into pFL2 vector by gap repair. This fusion plasmid was reintroduced into protoplasts of the ΔFomCFEM mutant to obtain complemented strains (ΔFomCFEM-C). G418-resistant transformants were screened and con rmed by PCR.
Characterization of Fom transformants To assay growth rate, the WT strain, FomCFEM deletion mutants, and FomCFEM-C transformants were cultured on PDA at 28℃ for 5 days. Then, the colony morphology and conidia of these strains were examined after being grown on PDA plate for 7 days. For stress tolerance assay, each indicated strain was inoculated onto CM plates containing 0.2 g·L − 1 Congo red (CR), 1 mol·L − 1 sorbitol, 0.05% SDS, 0.7 mol·L − 1 NaCl, 0.7 mol·L − 1 KCl, and 5 mmol·L − 1 H 2 O 2 as previously described [27,29]. To analyze the conidial germination, 50 µL conidial suspension (1 × 10 5 conidia·mL − 1 ) of each strain was spotted on hydrophobic coverslips and incubated at 28℃ for 12 h. Then, the conidial germination was examined by the Nikon Eclipse 90 i microscope (Nikon, Tokyo, Japan). Virulence assay of each strain on bitter gourd was performed as described in Sect. 2.6.

DNA and RNA extraction and sequencing
Metagenomic sequencing Total microbial genomic DNA from each soil sample was extracted from 0.5 g of soil using a FastDNA Spin kit (MP Biomedical, Santa Ana, California, USA) or DNeasyPowerSoil Kit (QIAGEN, Inc., Netherlands) according to the instruction provided by the manufacturer. The DNA quality was assessed on a NanoDrop spectrophotometer (Thermo Fisher Scienti c, Waltham, MA, USA). The extracted microbial DNA was processed to construct metagenome shotgun sequencing libraries with insert sizes of 400 bp by using the Illumina TruSeq Nano DNA LT Library Preparation Kit. Each library was sequenced by the Illumina HiSeq X-ten platform (Illumina, USA) with PE150 strategy. Raw sequencing reads were processed to obtain quality-ltered reads for further analysis. Co-occurrence networks were constructed according to Zhang [30].
Transcriptome sequencing Total RNA of fungal mycelium ( ltered through a lter paper) was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scienti c). Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were puri ed using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). The sequencing library was then sequenced on a Hiseq platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd. To quantify the identi ed gene expression in Fom, reference genome index was built by Bowtie2 (2.2.6) and the ltered reads were mapped to the Fusarium oxysporum f. sp. cubense race 1 (https://www.ncbi.nlm.nih.gov/genome/707? genome_assembly_id = 202328) reference genome using Tophat 2 (2.0.14), the default mismatch was no more than 2. We use HTSeq (0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM (fragments per kilobase of exon model per million mapped reads) to standardize the expression. Then we used DESeq (1.30.0) to analyze the genes of difference expression with screened conditions as follows: expression difference multiple | log 2 FoldChange| > 1, signi cant P-value < 0.05.

Validation of DEGs by RT-PCR
To con rm the transcriptome data, the genes were randomly selected and veri ed and their primers were designed using the Primer Premier 5.0 software listed in Supplementary Table S5. Quantitative reverse-transcription PCR (RT-PCR) was performed on a Light Cycler® 96 instrument (Roche) using SYBR Green qPCR kits (TaKaRa) according to the manufacturer's protocol. Reactions were performed at 95°C for 2 min, 45 cycles of 95°C for 10 s, 58°C for 30 s and 72°C for 30 s. EF1α was used as the reference genes. The relative expression levels of the target genes were calculated using the 2 −△△CT approach.

Statistical Analysis
All these experiments were carried out using three replicates and were repeated at least twice, with reproducible results. For multiple comparisons, two-way ANOVA with post hoc LSD and Duncan were performed using the SPSS 22.0.P < 0.05 was considered as signi cant.

Responses of soil physical-chemical properties and soil enzyme to the invasion of Fom
In this study, modi cations in physical-chemical properties and enzyme of the soil in which it was infected by Fom were described in Supplementary Table S6. The soil organic matter content (SOC), pH, electrical conductivity (EC), available nitrogen content (AN), available phosphorus content (AP) and available iron content (AFe) increased in S-FOM treatment. The signi cant increase in the value of SOC (57.7%), pH (2.0%), and AFe (27.7%) were obtained in S-FOM soil.
The control group had the higher values of soil uorescein diacetate (FDA) hydrolase and polyphenol oxidase (PPO). Although the inhibitory effects of different enzymes were different, the invasion of Fom signi cantly inhibited these enzymes. For example, the obvious decreases in the activities of FDA hydrolase (47.5%) and PPO (17.4%) were obtained in S-FOM soil. Soil FDA hydrolase and PPO activity were negatively correlated with the relative abundance of F. oxysporum, pH, organic matter content, and available Fe. This result indicated that the inhibition of F. oxysporum on enzyme activities of the soil might play critical roles in the conversion of organic matter and the change of pH.

Responses of community structure and diversity of soil to the invasion of Fom
The data set including 10 samples comprised a total of 22,492,589 contigs with 2,005,895 to 2,511,389 sequences per sample (mean 2,161,810.6 (Control) and 2,336,707.2 (S-FOM)) and 21,972,887 scaffolds with 1,931,781 to 2,469,478 sequences per sample (mean 2,106,715 (Control) and 2,287,862.4 (S-FOM)). A total of 6,923 microbes were assembled. The higher observed species and Chao1 index were detected for S-FOM, whereas the difference was not signi cant.
The Fom infected samples showed a signi cantly higher Simpson index and Shannon index of bacteria than Control, however, the Fom infected samples showed lower Simpson index and Shannon index of fungi than Control (Fig. 1A). When the beta diversity was assessed, the Control and S-FOM was signi cantly different (R 2 = 0.43,P = 0.013) ( Supplementary Fig. S1A). Redundancy analysis (RDA) revealed that the environmental factor variable possesses signi cant correlation with community structure. The variable of pH (R 2 = 0.65, P = 0.017) produced signi cant positive correlations with S-FOM microbes communities, the variable of FDA hydrolase (R 2 = 0.84, P = 0.002) and PPO (R 2 = 0.58, P = 0.043) produced signi cant negative correlations with S-FOM microbes communities ( Supplementary Fig. S1B).
The soil was predominantly colonized by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, Firmicutes, Nitrospirae, and Bacteroidetes, accounting for 63.0% of the total scaffolds, when the microbe was assessed at the phylum level (Fig. 1B). Ascomycota and Basidiomycota were the largest fungal taxonomic group, but accounted for a substantially lower proportion of microbe-assigned reads (Fig. 1D). The higher abundance of increased Proteobacteria, Firmicutes, and Nitrospirae were detected in the S-FOM samples that were subjected to invasion of F. oxysporum. Meanwhile, the obvious decreases in the relative abundance of Acidobacteria, Gemmatimonadetes, Planctomycetes, and Basidiomycota were obtained in S-FOM soil ( Fig. 1B and D). The modi cations in the composition of the core microbe at the genus level of the S-FOM samples were described in Fig. 1C, Fig. 1E, and Supplementary Fig. S1C. The invasion of Fom signi cantly in uenced these microbes, although the in uence differed in different microbes. For example, the obvious decreases in the relative abundance of Aspergillus, Pseudomonas, Sphingobium, Lysobacter, Variovorax, Sporisorium, Methylobacterium, Mycobacterium, Micromonospora, Actinoplanes, Mycolicibacterium, Amycolatopsis, Frankia, Pseudonocardia, and Ilumatobacter were obtained in S-FOM samples. Simultaneously, the relative abundance of Fusarium, Agromyces, Ramlibacter, Streptomyces, Conexibacter and Kribbella were signi cantly increased in S-FOM samples. Sphingomonas, Trichoderma, and Bacillus had no difference between the control sample and the S-FOM samples. At the species level, the relative abundance of Trichoderma asperellum, T. atroviride, Bacillus anthracis, B. kochii, Talaromyces stipitatus and so on showed an increased tendency in response to the invasion of F. oxysporum ( Supplementary Fig. S2). Meanwhile, Fusarium sp. was composed of F. incarnatum, F. culmorum, F. delphinoides, F. dimerum, F. equiseti, F. fujikuroi, F. graminearum, F. langsethiae, F. oxysporum, F. pseudograminearum, F. solani, F. venenatum, F. verticillioides, and Unclassi ed Fusarium. The F. oxysporum, F. solani, and F. fujikuroi showed signi cantly higher proportions than others. A signi cant increase of the relative abundance of F. oxysporum (51.7%) was observed in S-FOM samples, while there was no difference in other species.

Co-occurrence networks analysis of microbial communities
To study the effect of the invasion of Fom on microbial interactions, the networks were constructed ( Supplementary Fig. S3). The co-occurrence network was constructed from 10 samples (Control and S-FOM) based on the strong and signi cant (P < 0.05) correlations of microbial species. In total, 5035 nodes (5025 microbial nodes and 10 environmental nodes) and 17912 edges were shared among co-occurrence networks, and the co-occurrence networks contains 89.54%-92.13% microbial biomass (Supplementary Table S7). The degrees of the networks followed power-law distributions, the average path length was signi cantly larger than the corresponding random networks, which indicated that co-occurrence networks was a small world (Supplementary Fig. S2 and Table S7). Meanwhile, modularity values were higher than the random networks and greater than 0.34. This indicated that the co-occurrence networks had modular structures. For the networks, approximately 82.75% of the nodes belonged to bacteria, 7.98% of the nodes belonged to eukaryota, 7.36% of the nodes belonged to archaea, 1.91% of the nodes belonged to viruses. Proteobacteria (33.29%), Actinobacteria (18.23%), and Firmicutes (7.02%) accounted for more links in the network. There are 353 modules among the networks, of which 15 modules had more than 50 nodes, such as module 1141, module 676, module  1458, module 1465, module 168, module 1460, module 1229, module 1163, module 1124, module 1281, module 1250, module 1238, module 1225, module 1286 and module 1283, the nodes account for 37.87% of the total number of nodes and the relative abundance of microbe the nodes account for 70.39-75.23% of the total number of microbe, including Proteobacteria (35.26%), Actinobacteria (20.86%), Firmicutes (6.25%), Euryarchaeota (2.94%), Thaumarchaeota (2.73%), Ascomycota (2.47%), and Bacteroidetes (2.15%) ( Supplementary Fig. S3 C and D). We investigated the distribution of soil microbial species by Zi-Pi plot ( Supplementary Fig. S4). In the network, 94.22% of the nodes belong to the peripherals, 4.39% of the nodes belong to the connectors, 0.71% of the nodes belong to the module hubs, 0.08% of the nodes belong to the network hubs, among them, the connectors, module hubs and the network hubs were considered as key microorganisms. Among the 261 key microbial species, 159 microbial species belong to Proteobacteria, 27 microbial species belong to the Actinobacteria, and the relative abundance of 13 microbial species were increased in S-FOM samples ( Table 1). The relative abundance of sp1571 (Kribbella avida), sp1615 (Microlunatus soli), sp2002 (Streptomyces sp. 4F), sp4492 (Devosia sp.), sp5385 (Burkholderia sp.), sp5454 (Paraburkholderia sprentiae), sp5496 (Acidovorax sp.), sp5501 (Alicycliphilus denitri cans) and sp5675 (Chromobacterium vaccinii) were signi cantly positively correlated with the relative abundance of F. oxysporum. The relative abundance of sp5951 (Haliangium ochraceum), sp744 (Acidimicrobium ferrooxidans) and sp4354 (Bradyrhizobium erythrophlei) were negatively correlated with the relative abundance of F. oxysporum.  Table S1). The secondary screening was conducted in pot trials and successfully revealed 4 biocontrol agents that have strong control effects on Fusarium wilt of bitter gourd in the greenhouse, including bacterial strain SK2 and SK6, Talaromyces sp. strain Q2, and Trichoderma sp. strain M2, their control e cacy on Fusarium wilt were 68%-79% (Supplementary Table S8). Meanwhile, the relative abundance of sp1571 (Kribbella avida), sp2002 (Streptomyces sp. 4F), sp4492 (Devosia sp.), sp5496 (Acidovorax sp.), sp5501 (Alicycliphilus denitri cans), sp5675 (Chromobacterium vaccinii) and F. oxysporum were signi cantly positively correlated with the relative abundance of strain Q2, and the correlation coe cient between strain Q2 and F. oxysporum reaches 0.79 (Table 1).
Strain Q2 had great potential for biological control. For example, it was able to produce β-1, 3-glucanase and chitinase ( Fig. 2E and F).  Table S10). After co-culture for 5 days, obvious inhibitory zone was occurred between the colony of strain Q2 and Fom, which inhibited the mycelia growth of Fom by 65.86% ( Fig. 2A and Supplementary Table S10).

The control e cacy of strain Q2 on Fusarium wilt of bitter gourd
The control e cacy of strain Q2 on Fusarium wilt of bitter gourd was 63.4% (greenhouse) and 60.2% ( eld) ( Table 2). The disease incidence and disease index of bitter gourd seedlings were signi cantly decreased after treatment with strain Q2. Besides, the time of bitter gourd seedling infected by Fom was obviously postponed, which demonstrated that the resistance to Fusarium wilt of bitter gourd seedlings was enhanced after inoculation with strain Q2. Meanwhile, the obvious modi cations the composition of the fungal communities at the genus level of the Fom pathogenic soil treated with strain Q2 were discovered in this study ( Supplementary Fig. S7). The lower observed species and Chao1 index were detected in TP samples (The pathogenic soil with Fusarium inoculation was treated with antagonistic fungus T. purpureogenus strain Q2), whereas the difference was not signi cant, the TP samples showed a signi cantly lower Simpson index and Shannon index of fungi than S-FOM samples, but, the TP samples showed a signi cantly higher Simpson index and Shannon index of bacteria than S-FOM samples ( Supplementary Fig. S7A). The relative abundance of Actinobacteria, Firmicutes, Ascomycota, Chytridiomycota, Streptomyces, Conexibacter, Sphingomonas, Rhodoplanes, Gemmatirosa, Sphingobium, Nocardioides, Mesorhizobium, Lysobacter, Mycobacterium, Micromonospora, Talaromyces, Aspergillus, Thermothelomyces, and Chaetomium were increased in TP samples. The decreases in the relative abundance of Fusarium, Cordyceps, Colletotrichum, Anthracocystis, Trichoderma, Thielavia, Cladophialophora, Gaeumannomyces, Sporisorium, Verticillium, Fonsecaea, Exophiala, Trametes, and Diplodia were observed in TP samples ( Supplementary Fig. S7 B-E). Talaromyces became the largest fungal taxonomic group in the TP samples compared with S-FOM samples, the relative abundance of strain Q2 that obtained by comparing the genome of the strain Q2 to the metagenomic sequencing data in the TP samples was 2828.01 reads compared to S-FOM samples with 51.87 reads and control samples with 27.09 reads ( Supplementary Fig. S7E and I). A random forest analysis was then applied to identify the major microbes that contribute to the variation in soil microbiota. Ascomycota, Thaumarchaeota, Euglenida, Firmicutes, Chytridiomycota, Actinobacteria, Nitrospirae, Bacteroidetes, Microsporidia and so on were the primary factor that affected features of soil of microbial community ( Supplementary Fig. S7 F). Spearman's correlation network analyses con rmed that Actinobacteria, Ascomycota, Nitrospirae, Tenericutes, Bacteroidetes, Bathyarchaeota, Beckwithbacteria, Campbellbacteria, Saccharibacteria, Tectomicrobia, Woesebacteria, Wolfebacteria, Elusimicrobia, Thaumarchaeota and T. purpureogenus obviously in uenced the Simpson index of soil microbiota (Supplementary Table S12). Meanwhile, T. purpureogenus seems to have a strong positive correlation with Actinobacteria, Firmicutes, Thaumarchaeota, Ascomycota, Bacillariophyta, Bacteroidetes, Beckwithbacteria, Campbellbacteria, Saccharibacteria, Woesebacteria, Wolfebacteria, Elusimicrobia, and Tenericutes (Supplementary Table S12). The relative abundance of Fusarium decreased in the TP sample ( Supplementary Fig. S7G), but the number of Fusarium in the rhizosphere of bitter gourd had decreased signi cantly on the Fusarium selective medium (Komada's medium) (Supplementary Fig. S7H). The density of Fusarium under TP treatment was lower, with only 10,700 cfu·g − 1 soil compared to 17, 600 cfu·g − 1 soil in S-FOM treatment. Meanwhile, strain Q2 could colonize in soil, but its increasing trend in soil was gradually decreasing (Supplementary Fig. S7J). To constructed the co-occurrence network between Control, S-FOM and TP to explain the in uence F. oxysporum f. sp. momordicae (Fom) and T. purpureogenus (Tp) to soil microbiota ( Fig. 3A and 3B), we compared the differences in network-level topological features between Control, S-FOM and TP. For different treatments, soil pH was signi cantly lower in TP treatment than in Control and S-FOM. However, electrical conductivity (EC), available phosphorus (AP), available iron (AFe), available manganese (AMn), soil organic matter (SOC), FDA hydrolase, polyphenol oxidase (PPO), urease (UE) and acid phosphatase (ACP) were higher in TP treatment than in Control and S-FOM (Supplementary Table. S6). Similar to soil enzyme, values for the vertex number, edge number, modularity and degree centralization were signi cantly higher for sub-networks in TP treatment than in Control, according to Tukey HSD tests ( Fig. 3C). In contrast, values for the average path length and density were lower for sub-networks in TP treatment than in Control (Fig. 3C). These results suggest that the soil microbiota in TP treatment was more closely associated than in Control. To evaluate the relative contribution of soil chemical properties and soil enzyme activity to network-level topological features of the soil microbial network. In total, compared with soil chemical properties, the soil enzyme activity contributed to more of the variation in the network-level topological features. The contribution of soil FDA hydrolase, urease (UE), acid phosphatase (ACP), soil pH, available iron (AFe) and available manganese (AMn) to the network-level topological features overwhelmed that of other environmental factors with multiple regression analysis (Fig. 3D). Compared with F. oxysporum, T. purpureogenus seems to have a stronger positive correlation with vertex number, edge number, modularity and degree centralization and negative correlation with density based on Spearman's correlation analysis (Fig. 3E). Meanwhile, F. oxysporum and T. purpureogenus had a strong positive correlation with SOC, AFe, S-UE and S-ACP, and T. purpureogenus also have a strong positive correlation with EC and AP (Fig. 3E). The degrees of the networks followed power-law distributions indicated that co-occurrence networks was a small world ( Supplementary Fig. S8A). The co-occurrence network contained 1718 nodes (1717 microbial nodes and 1 environmental nodes), 3445 edges, and 72.73%-74.80% microbial biomass (Fig. 3). In the network, 98.72% of the nodes belong to the peripherals, 1.05% of the nodes belong to the connectors, and 0.17% of the nodes belong to the module hubs, according to the distribution of soil microbial species by Zi-Pi plot ( Supplementary Fig. S8B). Among the 1717 key microbial species, 33.93% microbial species belong to Proteobacteria, 20.9% microbial species belong to Actinobacteria, 6.52% microbial species belong to Firmicutes, 3.78% microbial species belong to Thaumarchaeota, 3.08% microbial species belong to Euryarchaeota, and 2.91% microbial species belong to Ascomycota ( Supplementary Fig. S8C). The relative abundance of Actinobacteria and Firmicutes were higher in TP treatment than in Control and S-FOM.   Fig. S9A). There are 1512 nodes, 33 phyla and 62.77%-64.63% microbial biomass in 13 larger modules ( Supplementary Fig. S9 C). T. purpureogenus participated in the construction of cooccurrence network as environmental factor. It showed signi cant negative correlations with the Acidobacteria, Firmicutes, Chloro exi Armatimonadetes, Chromerida, Chytridiomycota and Chlamydiae, obvious positive correlations with Actinobacteria and Dictyoglomi ( Supplementary Fig. S9 E). In contrast, F. oxysporum showed positive correlations with the Acidobacteria, Firmicutes, Chloro exi Armatimonadetes, Chromerida, Chytridiomycota and Chlamydiae, negative correlations with Actinobacteria and Dictyoglomi. Meanwhile, T. purpureogenus tended to co-occur with Actinobacteria and Proteobacteria of module 897. Module 897 was a module with Actinobacteria as the main component ( Supplementary Fig. S9 D). The microbial species, such as Kribbella avida, Frankia casuarinae, Kitasatospora setae, Nocardiopsis alba, Streptomyces niveus and Xylanimonas cellulosilytica, in module 897 were signi cantly positively correlated with the relative abundance of T. purpureogenus. The results indicated that T. purpureogenus strain Q2 involved in the resistance of soil microbial communities to the invasion of F. oxysporum, and the growth and development of F. oxysporum was inhibited by T. purpureogenus and its "friends".

Inhibition of the growth and development of Fom by strain Q2 in co-culture
To understand the mechanisms of inhibition of growth and development of Fom by strain Q2 under natural condition. In this study, the liquid co-cultivation of strain Q2 and Fom was rstly attempted, and the growth of strain Q2 and FOM in the axenic and co-culture conditions in PDB were signi cantly different at 48 h. It was observed that the culture liquor of FOM appeared beige, thicker, hazy mixture, while the color of culture liquor of strain Q2 was relatively lighter and appeared red white after they were singly-cultured for two days. However, when the inoculation ratio of strain Q2 and FOM was greater than 2:1, after cocultivation for two days, the culture broth color was red and deepened with time, and the mycelia of strain Q2 were dominant (Supplementary Fig. S10). Fom hyphae from the control group was not changed under the light microscope and hyphae grown and developed normally (Fig. 4A). Strain Q2 hyphae of all the groups were normally grown and developed, and the color of strain Q2 was not changed (Fig. 4A). There were morphological changes that hypha swelling appears round, the appearance of septa digestion, cytoplasma concentration and more than globular material in hypha cells of Fom compared with control group (Fig. 4A). Propidium iodide (PI) staining showed that the Fom conidia with red pigment accumulation lost vitality in T1 to T4 samples ( Fig. 4B and C).
The presence of propidium iodide and the red pigment in Fom cells indicated that the integrity of the cell wall and cell membrane of Fom were damaged. We investigated the effect of strain Q2 on malondialdehyde (MDA) concentration and triglyceride content of Fom cell. The results showed that the MDA content and triglyceride content of Fom cell increased in T1 to T4 samples compared to control (Fig. 4F and G). The MDA content and triglyceride content in T2 treatment were signi cantly higher than those in the control. At the same time, it is worth noting that the small fragments increased in the culture ltrate of T3 samples (Fig. 4B), and the N-acetylglucosamine (N-acetylglucosamine is a hydrolysate of chitin) content in the culture ltrate of T1 to T3 samples was signi cantly higher than that in the control (Fig. 4E), and the content of N-acetylglucosamine gradually increases with inoculation concentration of strain Q2 increases. The results indicated that strain Q2 maybe inhibit the growth and development of Fom by destroying the integrity of the cell wall and cell membrane of Fom.

The in uence of strain Q2 on the metabolic function of Fom at transcriptional level
A total of more than 336.47 million high quality clean reads were obtained after removing duplicate reads, trimming adapters and low quality sequences from six libraries. Q30 percentage was over 92% for all the samples. These data showed that the RNA-Seq quality was applicable for further analysis. In FOM samples, 89.20 % to 89.73 % of the total reads were mapped to the genome of F. oxysporum f. sp. cubense race 1; and more than 95 % of the reads in each sample were uniquely mapped to the genome. In Q2-FOM samples, 28.25 % to 47.17 % of the total reads were mapped to the genome of F. oxysporum f. sp. cubense race 1; and 96.86 % to 97.15% of the reads in each sample were uniquely mapped to the genome (Supplementary Table S13).
Differentially expressed genes (DEGs) were identi ed between FOM and Q2-FOM groups through comparing the expected read counts normalized using the DEseq package. To compare the expression levels of the DEGs between two groups, sequences count based differential expression analysis was performed. It was observed that 4,893 genes expression levels in FOM were identi ed as differentially expressed in FOM and Q2-FOM groups, including 2,435 up-regulated and 2,458 down-regulated ( Supplementary Fig. S11A). The Gene Ontology analysis (GO) and KEGG analysis of DEGs was further conducted (Supplementary (65 up-regulated genes and 146 down-regulated genes) groups. In the Q2-FOM groups, the genes associated with membrane and transport appeared to be the most signi cantly enriched. To further investigate the biochemical pathways of these DEGs in the process of T. purpureogenus inhibiting the growth of Fom, we mapped all DEGs identi ed in the RNA sequencing to terms in the KEGG database. The results showed the DEGs could be classi ed into four pathways, including metabolism, genetic information processing, environmental information processing and cellular processes. Top 20 enriched KEGG pathways associated with DEGs affected by T. purpureogenus were showed in Supplementary Fig. S11B, including glyoxylate and dicarboxylate metabolism, glutathione metabolism, valine, leucine and isoleucine degradation, glycerophospholipid metabolism, phenylalanine metabolism, nitrogen metabolism, propanoate metabolism, pyruvate metabolism, ABC transporters, galactose metabolism, tyrosine metabolism and glycerolipid metabolism. These results further indicated that stress of strain Q2 may greatly in uence carbohydrate metabolism, amino acid metabolism, lipid metabolism, energy metabolism, component of membrane and membrane transport of F. oxysporum.
We found a gene with CFEM domains (the characteristic eight cysteine residues at N terminus) and putative GPI-anchored site (FOC1 g10014283) in further analysis of differentially expressed genes. The expression level of FOC1 g10014283 was signi cantly decreased in Q2-FOM samples compared to FOM samples, although his function is unknown in F. oxysporum ( Fig. 6A and Supplementary Table S14). We experimentally isolated and characterized an FOC1 g10014283 orthologue, FomCFEM, in F. oxysporum f. sp. momordicae.

FomCFEM is important for full virulence and stress tolerance
The SMART-PFAM revealed that FomCFEM consists of a CFEM domain, a signal peptide, and the potential GPI-modi cation site (the amino acids N 291 and A 292 ) (Supplementary Fig. S12A and Supplementary Fig. S13). A phylogenetic analysis of the putative FomCFEM, homologous sequences of Fusarium and other fungal genes with CFEM domain indicated that homologous sequences of FomCFEM were common in Fusarium and the FomCFEM is closely homologous to the gene with CFEM domain from Trichoderma asperellum (GFP54046.1) (Supplementary Fig. S12B). To assess functions of FomCFEM, in F. oxysporum f. sp. momordicae by homologous recombination, FomCFEM deletion transformants harboring a hygromycin-resistance gene instead of the entire FomCFEM were generated. After PCR and Southern blot assays, the predicted FomCFEM separate mutants were obtained (Supplementary Fig. S12C and Fig.  S14B). One of the mutants (designated as ∆FomCFEM) was selected for complementation by reintroducing the entire FomCFEM gene under the control of its native promoter into the ∆FomCFEM mutant ( Supplementary Fig. S12D).
To determine the role of FomCFEM in pathogenicity, the rhizosphere soil of bitter gourd seedlings were inoculated with conidial suspensions of WT, ∆FomCFEM mutant, and ∆FomCFEM-C strains (the inoculation amount was 1×10 6 spores/g·soil). The disease incidence and disease index of bitter gourd seedlings were signi cantly decreased after treatment with ∆FomCFEM mutant (Fig. 6B and C). The ∆FomCFEM mutant resulted in a 58.8% reduction in virulence compared to the WT strain. These results suggest that FomCFEM is essential for full virulence in F. oxysporum f. sp. momordicae. Although conidial production of ∆FomCFEM was decreased compared with WT and ∆FomCFEM-C strains, there was no difference in the conidium morphology and conidial germination of ∆FomCFEM, WT, and ∆FomCFEM-C ( Fig. 6F-G). In addition, to investigate whether FomCFEM is involved in external stress tolerance, growth assays of indicated strains on CM media supplemented with salt stress (0.7 mol·L − 1 NaCl and 0.7 mol·L − 1 KCl), osmotic stress (1 mol·L − 1 sorbitol), H 2 O 2 (5 mmol·L − 1 ) and cell wall stress (0.05% SDS, and 0.2 g·mL − 1 CR) were analyzed, respectively. The results showed that the ∆FomCFEM strain was more hypersensitive to the cell wall stress compared with WT and ∆FomCFEM-C strain ( Fig. 6D and E). These results indicated that ∆FomCFEM may play an important role in the integrity and function of the cell wall of F. oxysporum f. sp. momordicae.

Discussion
Soil microbiota, including microbial biomass, communities, diversity and the abundance of speci c microbial groups, is seen to be critical for the maintenance of soil health, soil quality, and soil enzyme activities [6,31]. If the soil microorganisms are compared as the genetic material of the soil, each microbe is like the functional genes, and they are associated and interact with each other. However, pathogens of soil-borne disease, like cancer genes, seriously destroy microbical network and the health of the soil. The invasion of pathogens such as Ralstonia solanacearum and F. oxysporum would trigger drastic changes in the microbiome composition leading to the decline in disease suppression and soil quality represented by an increase in plant pathogens and loss of microbial diversity and community functioning, and once-invaded soil microbial communities could become more susceptible to secondary invasions during following crops seasons [32,33,34]. In our study, the implications of the exogenous F. oxysporum on the microbiome were primarily re ected by the changing pathogen of Fusarium wilt, microbial abundance, and microbial diversity. While the invasion of exogenous F. oxysporum increased fungal abundance and bacterial diversity, the relative abundance of the microbial species showed a different change. The previous investigations also reported that fungal diversity differed signi cantly between the suppressive and conducive soils, high soil fungal richness signi cantly correlated to a higher Fusarium wilt [5,32]. The relative abundance of F. oxysporum f. sp. cubense, fungal or bacterial richness and diversity were higher in the diseased soils than in the disease-free soils [34]. It has been proved that pathogens were strongly restricted in growth by the activities of speci c rhizosphere microorganisms. Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae, and Sphingomonadaceae were signi cantly more abundant in the rhizosphere upon the invasion of R. solani in disease-suppressive soils [35]. Suppressive soils provide the best examples of natural microbe-based defense the invasion of pathogens, whereby via the soil microorganisms build up the rst line of defense against soilborne pathogens. However, it is unknown what kind of army that built up by soil microorganisms defense against soilborne pathogens when the inoculum of a soilborne pathogen is added to an unamended or raw eld soil. We attempted to understand how indigenous microbiomes can reduce the occurrence of Fusarium wilt, even in the conducive soils. When it was assessed in more detail, we found that the invasion of F. oxysporum signi cantly oppressed the growth of the dominant microbes and activated the growth of non-dominant microbes. The relative abundance of Gemmatimonadetes, Bradyrhizobium, Luteitalea, Conexibacter, Rhodoplanes, Cordyceps, Gemmatirosa, Aspergillus, and Thielavia decreased in S-FOM samples, while the relative abundance of many non-dominant microbes increased in S-FOM samples, such as Kribbella sp., Devosia sp., Alicycliphilus sp., Chromobacterium sp., Talaromyces sp., and Streptomyces sp.(dominant microbes). The relative abundance of Trichoderma and Bacillus that have been widely used as a biological control agent against various pathogens were no difference between control samples and S-FOM samples [15,16,17,18]. But, the relative abundance of T. asperellum, T. atroviride, B. anthracis, B. kochii, and so on showed an increased tendency in response to the invasion of F. oxysporum. Microbes response to invasive F. oxysporum, and these population dynamics have diverse consequences for microbial tness, microbial community structure, and soil functional. The interactive patterns within microbes and F. oxysporum may be positive (mutualism, synergism, or commensalism), negative (predation, parasitism, antagonism, or competition), or neutra. We attempted to shed light on the interactive relevance between the variable tendency of microbes and F. oxysporum, and found the biocontrol agent from these changed indigenous microorganisms, although it is unknown that the role of these microorganisms plays in the defense against the invasion of Fusarium. We speculated that these microbes with an increase tendency may be associated with suppression of Fusarium wilt.
Biological control has gained a great contribution to control Fusarium wilt in the last years [36]. A large number of biological control agents (BCAs) with variable effectiveness against F. oxysporum have been applied [37,38], and many of them reached the stage of eld trials [39]. But most biocontrol fungi are still in the theoretical or conceptual stage owing to several factors including stability in eld and di culty in solid fermentation. Obtaining these biocontrol fungi with stable biocontrol effect and easy fermentation are the main factor for their successful application. In our study, we obtained 14 biocontrol agents with strong antagonistic activity to F. oxysporum on plate, originally separated from the pathogenic soil of Fusarium wilt. In the comprehensive evaluation of the 14 biocontrol agents, we found T. purpureogenus strain Q2 had more stable and constant biocontrol e cacy on Fusarium wilt than Trichoderma and Bacillus in the greenhouse and eld and the strain Q2 could stably colonize in the soil. Meanwhile, the strain Q2 showed the biocontrol potential against various pathogenic fungi, especially F. oxysporum. However, the biocontrol strains (bacteria or fungi) with an antagonistic effect on pathogen propagule initiate sustained disease suppression after reaching threshold population sizes (10 5 cfu/g) [40]. In our study, the Fusarium wilt still occurred, although the relative abundance of strain Q2 increased in the process of F. oxysporum invading the soil, this does not prove that the total microbiome including strain Q2 did not contribute to reduce the incidence of Fusarium wilt. The strain Q2 reached the threshold of population sizes (1×10 6 cfu/g) by human intervention and started continuous disease suppression through inhibiting the growth and development of F. oxysporum. This has also been observed during the co-culture of strain Q2 and F. oxysporum f. sp. momordicae. Meanwhile, the strain Q2 can also excite the activity of other bene cial microorganisms such as actinomycetes. These results show that strain Q2 directly or indirectly suppresses the growth of F. oxysporum in the soil, and strain Q2 may be just the key player, other microbes play a supporting role.
Talaromyces species have a wide range of applications and are often used to produce enzymes and pigments in agriculture and industry. Talaromyces sp. has a higher number of proteins with carbohydrate-active enzyme (CAZymes) than other sequenced Penicillium based on sequencing of genome [41][42][43]. This indicates that Talaromyces sp. has stronger biological potential than Penicillium sp.. Talaromyces sp. as a potential biological control agent against fungal plant pathogen can be traced back to 1989 [44]. T. avus isolates from the ginseng seed was very effective applications in improving dehiscence and germination and showed antagonistic activities against fungal plant pathogens, such as Cylindrocarpon destructans, Rhizoctonia solani, Sclerotinia nivalis, Botrytis cinerea, and Phytophthora capsici [45]. In our work, we found strain Q2 can grow on a variety of nitrogen source such as beef extract, carbamide, peptone, ammonium chloride, ammonium sulfate and ammonium nitrate, and carbon source such as glucose, starch, lactose, maltose, sucrose, D-furctose.
Strain Q2 also have high tolerance to acid and temperature conditions, was able to soundly grow under the conditions of temperature ranged from 15 to 45 ℃ and pH 4-10. Meanwhile, strain Q2 has a higher number of CAZymes than other sequenced P. purpurogenum MYA-38 and can secrete the cell wall-degrading enzymes including β-1, 3-glucanase and chitinase [41]. Strain Q2 could produce more β-1, 3-glucanase and chitinase in culture medium containing cell wall fragments of F. oxysporum. Digestion of the fungal cell wall by microbial chitinase, chitosanase, and β-1, 3-glucanase may be one of mechanisms for biocontrol of soil-borne plant pathogens [17,[46][47][48]. Two strains of Clostridium beijerinckii can produce the cell wall-degrading enzymes and have the ability to kill F. oxysporum f. sp. spinaciae [48]. To understand the interaction of the strain Q2 and Fom, we initially conducted a co-cultivation with strain Q2 and Fom. The result showed that growth of Fom was signi cantly inhibited in the presence of strain Q2. In addition, β-1, 3-glucanase and chitinase enzymes production was improved in a combination inoculated with strain Q2 and Fom. Similarly, Copete-Pertuz identi ed a triple combination inoculated with Trichoderma viride and Aspergillus sterreus into a 7th day pre-culture of Leptosphaerulina sp. improved ligninolytic enzymes production when compared to the Leptosphaerulina sp. monoculture [49]. Meanwhile, our results showed that the content of malondialdehyde (MDA) and chitin of F. oxysporum mycelia had changed under the presence of strain Q2. This indicated that the change of the membrane permeability and cell wall structure of F. oxysporum hypae, and the damage degree of membrane system and cell wall was increased with the increase of strain Q2 density. The study on transcriptomes also brought useful information on the interaction between strain Q2 and Fom. RNA-seq data indicated that F. oxysporum membrane components, as well as transmembrane transport, seemed to have been seriously affected by the strain Q2 at the transcriptome level. The inhibitions observed on both growth and membrane function of Fom in our study were in accordance with those of Strub [50]. The membrane components and transmembrane transporter of F. verticillioides were affected by Streptomyces sp. AV05 during their co-cultivation [50].
In the model fungus Saccharomyces cerevisiae, the cell wall and cell membrane play an important role that it's de ning cell shape during growth, mating, sporulation; and presents adhesive glycoproteins to other yeast cells [51,52]. In the fungal plant pathogen F. oxysporum, the integrity of the cell wall and cell membrane not only plays an important role in mycelium growth but also associated with plant interaction [53]. In our study, we discovered that several pathways associated with cell wall morphogenesis, such as starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism and GPI biosynthesis were drastically in uenced by strain Q2. In the further analysis of the transcriptional pro ling, large numbers of genes associated with Fom cell integrity were down-regulation, including the cell wall relating genes and cell membrane relating genes, have been proved to play an important role in the fungal growth and pathogenicity [54]. In this work, the expression level of cell wall and cell membrane relating genes decreased signi cantly, such as CHS1, CHS2, CHS3, CHS7, YEA4, GPI1, GPI2, GPI15, GPI12, SMP3 and GPI18. CHS7 is a limiting factor in the export of CHS3, CHS7 deletion leads to CHS3 aggregates in the ER and reduces chitin synthase III (CSIII) activity [55,56]. YEA4 is the second ER membrane protein with UDP-GlcNAc transport activity, whose transport activity contributes to chitin synthesis [57]. GPI-anchored proteins, which anchored to the outer layer of the plasma membrane through a C-terminal GPI anchor, are essential for growth, viability, morphogenesis, signaling transmission, reproduction and disease pathogenesis in all eukaryotic cells [58][59][60]. GPI1, GPI15, and GPI2 are core subunits of GPI-GlcNAc transferase complex, initiate the GPI biosynthesis. SMP3 and GPI18 are involved in GPI mannosylation. GPI12 catalyzes N-acetylglucosaminyl phosphatidylinositol de-N-acetylated, form glucosaminyl phosphatidylinositol. Once the GPI biosynthesis is blocked, the growth and development of the fungus will be affected. Meanwhile, multiple GPI-modi ed wall proteins of the fungus were important to osmotic stability and mortality [29]. In this study, we isolated and characterized a CFEM protein FomCFEM (homologous sequences of FOC1 g10014283) with a putative GPI modi cation site from F. oxysporum f. sp. momordicae. Nevertheless, the speci c roles of the FomCFEM in F. oxysporum remain largely unknown. According to the results which we had obtained, the FomCFEM deletion mutant strain was more hypersensitive to the cell wall and stress tolerance compared with WT and ∆FomCFEM-C strains, indicating that FomCFEM positively regulate the tolerance of F. oxysporum f. sp. momordicae to osmotic stabilizers. Meanwhile, the FomCFEM plays an important role in the full virulence of F. oxysporum f. sp. momordicae. Similar result had also been reported in other studies that the gene with CFEM domain and putative GPI-anchored site involved in virulence, conidiation and stress tolerance of Botrytis cinerea [29]. Therefore, strain Q2 suppresses the expression level of FomCFEM, which may be play an important role in the prevention and control of Fusarium wilt.
T. purpureogenus strain Q2 was a soil and rhizosphere microorganisms, isolated from the rhizosphere of healthy plant that planted in the pathogenic soil of F.oxysporum. In the present study, strain Q2 has antagonistic activity against a variety of pathogens, especially against F. oxysporum and has a good control effect on Fusarium wilt of bitter gourd. Our results indicated that the mechanisms of strains Q2 protected bitter gourd was to reduce the relative abundance of rhizospheric F.oxysporum by direct and indirect inhibiting the growth and development of F. oxysporum, because the positive correlations were found between the disease incidence and growth degree of F. oxysporum [61]. In summary, strain Q2 was a good strain with the potential for biological control of Fusarium wilt. This work could provide a new potential biocontrol agent for the biocontrol of Fusarium wilt and soil-born diseases of other horticultural crops.

Conclusions
Our study demonstrates that we have screened a e cient biocontrol agents, Talaromyces purpurogenus strain Q2, from microorganisms with resistance to the invasion of F. oxysporum. The biocontrol mechanisms of T. purpurogenus strain Q2 protected bitter gourd from F. oxysporum is to reduce the relative abundance of rhizospheric F. oxysporum by inhibiting the growth and development of F. oxysporum. This work can provide a new biocontrol agent for biocontrol of Fusarium wilt and soil-born diseases of other horticultural crops.  The morphological characteristics and biocontrol function of bene cial microorganisms strain Q2 Figure 3 Co-occurrence networks of soil communities constructed from Control, S-FOM and TP based on correlation analysis Figure 4 The effects of strain Q2 on the growth and reproduction of Fom during interactions between T. purpureogenus strain Q2 and Fom Figure 5 The effects of strain Q2 on the metabolic pathways and related gene expression of Fom during interactions between T. purpureogenus strain Q2 and Fom