Fusarium crown rot (FCR) caused by Fusarium pseudograminearum is one of the most serious soil-borne diseases of wheat. Among 58 bacterial isolates from the rhizosphere soil of winter wheat seedlings, strain YB-1631 was found to have the highest in vitro antagonism to F. pseudograminearum growth. LB cell-free culture filtrates inhibited mycelial growth and conidia germination of F. pseudograminearum by 84.14% and 92.23%, respectively. The culture filtrate caused distortion and disruption of the cells. Using a face-to-face plate assay, volatile substances produced by YB-1631 inhibited F. pseudograminearum growth by 68.16%. In the greenhouse, YB-1631 reduced the incidence of FCR on wheat seedlings by 84.02% and increased root and shoot fresh weights by 20.94% and 9.63%, respectively. YB-1631 was identified as Bacillus siamensis based on the gyrB sequence and average nucleotide identity of the complete genome. The complete genome was 4,090,312 bp with 4357 genes and 45.92% GC content. In the genome, genes were identified for root colonization, including those for chemotaxis and biofilm production, genes for plant growth promotion, including those for phytohormones and nutrient assimilation, and genes for biocontrol activity, including those for siderophores, extracellular hydrolase, volatiles, nonribosomal peptides, polyketide antibiotics, and elicitors of induced systemic resistance. In vitro production of siderophore, β-1, 3-glucanase, amylase, protease, cellulase, phosphorus solubilization, and indole acetic acid were detected. Bacillus siamensis YB-1631 appears to have significant potential in promoting wheat growth and controlling wheat FCR caused by F. pseudograminearum.

Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.

The use of biological control agents (BCAs) is a promising alternative control measure for Fusarium crown rot (FCR) of wheat caused by Fusarium pseudograminearum. A bacterial strain, YB-185, was isolated from the soil of wheat plants with FCR and identified as Bacillus velezensis. YB-185 exhibited strong inhibition of F. pseudograminearum mycelial growth and conidial germination in culture. Seed treatment with YB-185 in greenhouse and field resulted in reductions in disease by 66.1% and 57.6%, respectively, along with increased grain yield. Microscopy of infected root tissues confirmed that YB-185 reduced root invasion by F. pseudograminearum. RNA-seq of F. pseudograminearum during co-cultivation with B. velezensis YB-185 revealed 5086 differentially expressed genes (DEGs) compared to the control. Down-regulated DEGs included genes for glucan synthesis, fatty acid synthesis, mechanosensitive ion channels, superoxide dismutase, peroxiredoxin, thioredoxin, and plant-cell-wall-degrading enzymes, whereas up-regulated DEGs included genes for chitin synthesis, ergosterol synthesis, glutathione S-transferase, catalase, and ABC transporters. In addition, fungal cell apoptosis increased significantly, as indicated by TUNEL staining, and the scavenging rate of 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical cation (ABTS·+) in the fungus significantly decreased. Thus, F. pseudograminearum may be trying to maintain normal cell functions by increasing cell wall and membrane synthesis, antioxidant and anti-stress responses, detoxification of bacterial antimicrobial compounds, and transportation of damaging compounds from its cells. However, cell death and free radical accumulation still occurred, indicating that the responses were insufficient to prevent cell damage. Bacillus velezensis YB-185 is a promising BCA against FCR that acts by directly damaging F. pseudograminearum, thus reducing its ability to colonize roots and produce symptoms.

Wheat is a worldwide staple food crop, and take-all caused by Gaeumannomyces graminis var. tritici can lead to a tremendous decrease in wheat yield and quality. In this study, strain YB-10 was isolated from wheat rhizospheric soil and identified as Pseudomonas chlororaphis by morphology and 16S rRNA gene sequencing. Pseudomonas chlororaphis YB-10 had extracellular protease and cellulase activities and strongly inhibited the mycelium growth of Gaeumannomyces graminis var. tritici in dual cultures. Up to 87% efficacy of Pseudomonas chlororaphis YB-10 in controlling the take-all of seedlings was observed in pot experiments when wheat seed was coated with the bacterium. Pseudomonas chlororaphis YB-10 was also positive for indole acetic acid (IAA) and siderophore production, and coating wheat seed with the bacterium significantly promoted the growth of seedlings at 10⁷ and 10⁸ CFU/mL. Furthermore, treatment with Pseudomonas chlororaphis YB-10 increased activities of the wheat defense-related enzymes POD, SOD, CAT, PAL and PPO in seedlings, indicating induced resistance against pathogens. Overall, Pseudomonas chlororaphis YB-10 is a promising new seed-coating agent to both promote wheat growth and suppress take-all.

Maize (Zea mays L.) is the most widely grown crop in China, which was planted 41.28 million hectares in 2019 (http://data.stats.gov.cnw/easyquery.htm?cn=C01&zb=A0D0F&sj=2019). Several fungal diseases of maize are reported in which stalk rot has become one of the most destructive diseases in China. The average yield losses affected by the disease are estimated at 10% to 20% (Yu et al. 2016). From 2017 to 2019, a survey was conducted to determine the population diversity of Fusarium species associated with maize diseases in 18 cities across Henan province. Fusarium stalk rot of maize with disease incidence more than 25% was observed in two continuous maize fields at Xuchang city. The diseased stem tissues from junctions in health and disease were chopped into small pieces (3 × 8 mm), superficially disinfected (70% ethyl alcohol for 1 min), placed onto potato dextrose agar (PDA) amended with L-(+)-Lactic-acid (1 g/L), poured in petri plates and incubated at 25°C for 4 days. Mycelia showing morphological characteristic of Fusarium spp. were sub-cultured from single conidium. The pure fungal isolates produced fluffy colonies, white aerial mycelium with yellow pigment in agar. The radial mycelial growth was measured and calculated at an average growth rate 10.9 mm/day at 25°C (Fig. 1A; 1B). Macroconidia produced on carnation leaf agar (CLA) were relatively slender, slightly curved and thick-walled, mostly 3 to 5 marked septa, with a curved and tapering apical cell and poorly developed foot cell, 46.9 ± 5.6 µm × 4.9 ± 0.2 µm (Fig. 1C). Microconidia formed abundantly and were generally oval on CLA, 8.2 ± 0.5 µm × 3.4± 0.1 µm (Fig. 1D). No chlamydospores were observed. Morphological characteristics of the isolates matched the description of Fusarium thapsinum (Leslie and Summerell 2006). To further get the phylogenetic evidence, TEF1-α (translation elongation factor), RPB1 (the largest subunit of RNA polymerase II) and RPB2 (the second largest subunit of RNA polymerase II) were amplified with primer pairs EF1/EF2 (O'Donnell et al. 1998), thapR1F (5'-TTTTCCTCACAAAGGAGCAAATCATG-3')/thapR1R (5'-GTTCACCCAAGATATGGTCGAAAGCC-3'), and thapR2F (5'-ACTCTTTCACATTTGCGCCGAAC-3')/thapR2R (5'-CGGAGCTTTCGTCCAGTGTGAC-3'), and sequenced, respectively. The BLAST search of the sequences of EF1-α, RPB1 and RPB2 shared 99.87% to 100% identity with those of F. thapsinum strains deposited in the GenBank (Supplementary Table 1). Sequences from two isolates (XCCG-3-B-1 and XCCG-3-A-1) were deposited in GenBank (Accession No. MT550014, MT997082 for EF-1α; MT550011, MT997087 for RPB1 and MT550008, MT997091 for RPB2). The phylogenetic relationships based on analysis of the partial sequences showed the representive isolates clustered together with F. thapsinum at 96% bootstrap values (Fig. 2). Combined with the results of morphological characteristics and phylogenetic analysis, the strain designated as Fusarium thapsinum. To complete Koch's postulates, the pathogenicity of the isolates was tested using the silking-stage plants in a greenhouse based on previously described method with modification (Zhang et al. 2016). An 8 mm in diameter wound hole was created at the second or third internode of the plant above the soil surface and injected with 0.5 ml of mycelia plug. The inoculated stalk exhibited internal dark brown necrotic regions and the brown area elongated obviously around the insertion at 14 dpi (days post inoculation). At 30 dpi, the stalks turned soft, hollow and even lodging of the plants for those severe ones, which are similar to those observed on naturally infected maize plants in the field (Fig. 1F). When the roots of the three-leaf-stage seedlings were inoculated with 1×106 macroconidia solution (Ye et al. 2013), the root rot and leaf wilting symptoms were observed (Fig. 1E). While the control plants that were inoculated with only sterile water showed no disease symptoms. The pathogen was re-isolated from the inoculated tissues and the identity was confirmed by the morphological characters. Fusarium thapsinum had been described as causal agent of maize stalk rot in Pakistan (Tahir et al. 2018). To our knowledge, this is the first report of F. thapsinum associated with maize stalk rot in China. The discovery will strengthen the theoretical foundation of maize stalk rot disease management.

A total of 34 strains of bacteria were isolated from peanut rhizosphere soil, and all showed some in vitro inhibition of the pathogen Sclerotium rolfsii in co-culture. Strain YB-1632 produced the highest level of inhibition and also produced relatively high levels of biofilm in culture. Cell-free culture extracts and volatiles from it were also inhibitory to S. rolfsii. Based on 16S rDNA, gyrA, and gyrB sequences, it was identified as Bacillus siamensis. In the greenhouse, seed treatment resulted in a level of control of peanut sclerotium blight (PSB) comparable to that of a standard fungicide seed treatment. In addition to its antifungal activity, YB-1632 could induce disease resistance in peanut seedlings based on increasing peanut defense enzyme activities and gene expression. The priming of defense gene expression against a necrotrophic pathogen is consistent with Induced Systemic Resistance (ISR). In addition, YB-1632 produced enzyme activities in culture associated with root colonization and plant growth promotion. In the greenhouse, it increased peanut seedling growth, indicating the YB-1632 is a plant growth-promoting rhizobacterium (PGPR). In summary, YB-1632 is a promising novel PSB biocontrol agent and PGPR of peanut.