Enhancing defense against rice blast disease: Unveiling the role of leaf endophytic firmicutes in antifungal antibiosis and induced systemic resistance

Biocontrol Potential of Endophytic Bacillus velezensis LSR7 Against Rubber Red Root Rot Disease

To obtain an effective bacterial biocontrol strain against the fungal pathogen Ganoderma pseudoferreum, causing rubber tree red root rot disease, healthy rubber tree tissue from Baisha County, Hainan Province, was selected as the isolation source, and bacterial strains with strong antifungal effects against G. pseudoferreum were screened. The strain was identified by molecular biology, in vitro root segment tests, pot growth promotion tests, and genome detection. The strain was further evaluated by biological function tests, genome annotation analysis, and plant defense-related enzyme activity detection. The results show that strain LSR7 had good antagonistic effects against G. pseudoferreum, and the inhibition rate reached 88.49%. The strain LSR7 was identified as Bacillus velezensis by genome sequencing. In a greenhouse environment, LSR7 prevents and treats red root rot disease in rubber trees and promotes the growth of rubber tree seedlings. LSR7 secreted cell wall hydrolases (protease, glucanase, and cellulase), amylases, and siderophores. LSR7 also formed biofilms, facilitating plant colonization. Genome prediction showed that LSR7 secreted multiple antifungal lipopeptides. LSR7 enhanced rubber tree resistance to G. pseudoferreum by increasing the activity of defense enzymes. Bacillus velezensis LSR7 has biocontrol potential and is a candidate strain for controlling red root rot disease in rubber trees.

Roles of Phyllosphere Microbes in Rice Health and Productivity

The phyllosphere, comprising the aerial portions of plants, is a vibrant ecosystem teeming with diverse microorganisms crucial for plant health and productivity. This review examines the functional roles of phyllosphere microorganisms in rice (Oryza sativa), focusing on their importance in nutrient uptake, disease resistance, and growth promotion. The molecular mechanisms underlying these interactions are explored along with their potential applications in enhancing sustainable rice production. The symbiotic relationships between rice plants and their associated microorganisms are highlighted, offering insights into improved agricultural practices. Furthermore, this review addresses the challenges and future developments in translating laboratory findings into practical applications. By synthesizing current research, this comprehensive analysis serves as a valuable resource for leveraging phyllosphere microbes in rice farming and related fields.

AISOA-SSformer: An Effective Image Segmentation Method for Rice Leaf Disease Based on the Transformer Architecture

Rice leaf diseases have an important impact on modern farming, threatening crop health and yield. Accurate semantic segmentation techniques are crucial for segmenting diseased leaf parts and assisting farmers in disease identification. However, the diversity of rice growing environments and the complexity of leaf diseases pose challenges. To address these issues, this study introduces an innovative semantic segmentation algorithm for rice leaf pests and diseases based on the Transformer architecture AISOA-SSformer. First, it features the sparse global-update perceptron for real-time parameter updating, enhancing model stability and accuracy in learning irregular leaf features. Second, the salient feature attention mechanism is introduced to separate and reorganize features using the spatial reconstruction module (SRM) and channel reconstruction module (CRM), focusing on salient feature extraction and reducing background interference. Additionally, the annealing-integrated sparrow optimization algorithm fine-tunes the sparrow algorithm, gradually reducing the stochastic search amplitude to minimize loss. This enhances the model's adaptability and robustness, particularly against fuzzy edge features. The experimental results show that AISOA-SSformer achieves an 83.1% MIoU, an 80.3% Dice coefficient, and a 76.5% recall on a homemade dataset, with a model size of only 14.71 million parameters. Compared with other popular algorithms, it demonstrates greater accuracy in rice leaf disease segmentation. This method effectively improves segmentation, providing valuable insights for modern plantation management. The data and code used in this study will be open sourced at https://github.com/ZhouGuoXiong/Rice-Leaf-Disease-Segmentation-Dataset-Code.

Quality analysis and function prediction of soil microbial communities of Polygonatum cyrtonema in two indigenous-origins

Polygonatum cyrtonema Hua (PCH), as an important economic crop, is used as raw industrial materials and traditional Chinese medicine. There are significant variations in the quality of PCH from different geographical origins. It can be due to the change of the endophytic fungi and soil microbial communities of PCH. Therefore, the aim of this study is to investigate the composition and functional prediction of the main microbial communities in the rhizomes and soil of PCH and explore their impact on medicinal quality. High-throughput sequencing techniques targeting ITS and 16S rDNA were employed to compare the structure and biodiversity differences of endophytic fungi in the rhizomes and soil microbial communities of PCH from 12 different locations in Sichuan and Guangxi province. Heatmap analysis was used for comprehensive statistics and visualization of the richness of rhizome and soil microbial communities from all locations. Venn analysis was conducted to determine the total number of shared fungi between rhizomes and soil, and GraphPad Prism analysis was employed to predict and compare the microbial communities related to phenotypes at the genus level in Sichuan and Guangxi. Tax4Fun and Fungild were used for metabolic function prediction of microbial communities in the rhizomes and soil of PCH. The results revealed the identification of 19,387 bacterial amplicon sequence variants (ASVs) in the rhizomes and 37,990 bacterial ASVs in the soil, with 6,889 shared bacterial ASVs. In addition, 2,948 fungal ASVs were identified in the rhizomes and 8,868 in the soil, with 1,893 shared fungal ASVs. Microbial sequencing results indicated that the fungal communities between soil and rhizomes were mainly composed of Ascomycota and Basidiomycota, while bacterial communities included Proteobacteria, Acidobacteria, Bacteroidota, Gammatimonadota, and Firmicutes. Dominant bacterial groups such as Nitrospira, Acidibacter, and fungal groups including Mortierella, Ceratobasidium, and Fusarium were identified as potential contributors to the observed traits. In the top 15 microbial genera, both Sichuan and Guangxi contain 15 bacterial genera, but there are differences in their abundance. Guangxi has three unique fungal genera, including the genera Scleroderma, Russula, and Gliocladiopsis. On the other hand, Sichuan has the unique fungal genus Chamaeota. The correlation analysis between the microbiota and the chemical content from 12 different collecting spots was performed by GraphPad Prism. Burkholderia-Caballeronia-Paraburkholderia, Acidibacter, and Amycolatopsis show an inverse proportionality to total polysaccharides and saponins, while Enterobacter shows a direct proportionality to total polysaccharides and inverse proportionality to saponins. The metabolism pathways show a significant positive correlation with PCH polysaccharides and saponins. This study provide new insights into the mechanisms underlying the quality differences between the two major indigenous areas.

Effects of Bacillus subtilis on Cucumber Seedling Growth and Photosynthetic System under Different Potassium Ion Levels

Potassium deficiency is one of the important factors restricting cucumber growth and development. This experiment mainly explored the effect of Bacillus subtilis (B. subtilis) on cucumber seedling growth and the photosynthetic system under different potassium levels, and the rhizosphere bacteria (PGPR) that promote plant growth were used to solubilize potassium in soil, providing theoretical support for a further investigation of the effect of biological bacteria fertilizer on cucumber growth and potassium absorption. "Xinjin No. 4" was used as the test material for the pot experiment, and a two-factor experiment was designed. The first factor was potassium application treatment, and the second factor was bacterial application treatment. The effects of different treatments on cucumber seedling growth, photosynthetic characteristics, root morphology, and chlorophyll fluorescence parameters were studied. The results showed that potassium and B. subtilis had obvious promotion effects on the cucumber seedling growth and the photosynthesis of leaves. Compared with the blank control, the B. subtilis treatment had obvious effects on the cucumber seedling height, stem diameter, leaf area, total root length, total root surface area, total root volume, branch number, crossing number, gs, WUE, Ci, and A; the dry weight of the shoot and root increased significantly (p ≤ 0.05). Potassium application could significantly promote cucumber growth, and the effect of B. subtilis and potassium application was greater than that of potassium application alone, and the best effect was when 0.2 g/pot and B. subtilis were applied. In conclusion, potassium combined with B. subtilis could enhance the photosynthesis of cucumber leaves and promote the growth of cucumber.

Impact of bacterial volatiles on the plant growth attributes and defense mechanism of rice seedling

Rice is a major dietary element for about two billion people worldwide and it faces numerous biotic and abiotic stress for its cultivation. Rice blast disease caused by Magnaporthe oryzae reduce up to 30 % rice yield. Overuse of synthetic chemicals raises concerns about health and environment; so, there is an urgent need to explore innovative sustainable strategies for crop productivity. The main aim of this study is to explore the impact of bacterial volatiles (BVCs) on seedling growth and defense mechanisms of rice under in-vitro condition. On the basis of plant growth promoting properties, six bacterial strains were selected out of ninety-one isolated strains for this study; Pantoea dispersa BHUJPVR01, Enterobacter cloacae BHUJPVR02, Enterobacter sp. BHUJPVR12, Priestia aryabhattai BHUJPVR13, Pseudomonas sp. BHUJPVWRO5 and Staphylococcus sp. BHUJPVWLE7. Through the emission of bacterial volatiles compounds (BVCs), Enterobacter sp., P. dispersa and P. aryabhattai significantly reduces the growth of rice blast fungus Magnaporthe oryzae by 69.20 %, 66.15 % and 62.31 % respectively. Treatment of rice seedlings with BVCs exhibited significant enhancement in defence enzyme levels, including guaiacol peroxidase, polyphenol oxidase, total polyphenols, and total flavonoids by a maximum of up to 24 %, 48 %, 116 % and 80 %, respectively. Furthermore, BVCs effectively promote shoot height, root height, and root counts of rice. All BVCs treated plant showed a significant increase in shoot height. P. dispersa treated plants showed the highest increase of 60 % shoot and 110 % root length, respectively. Root counts increased up to 30% in plants treated with E. cloacae and Staphylococcus sp. The BVCs can be used as a sustainable approach for enhancing plant growth attributes, productivity and defence mechanism of rice plant under biotic and abiotic stresses.

Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens

BACKGROUND

Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36 found to have beneficial traits including plant growth promotion and broad-spectrum antifungal activity towards taxonomically diverse plant pathogens. Understanding the genomes will assist in devising a bioformulation for crop protection while exploiting their beneficial functional roles.

RESULTS

Two potential firmicute species were isolated from pearl millet panicles. Morphological, biochemical, and molecular characterization revealed their identities as Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36. The seed priming assays revealed the ability of both species to enhance plant growth promotion and seedling vigour index. Invitro assays with PBs 12 and PBl 36 showed the antibiosis effect against taxonomically diverse plant pathogens (Magnaporthe grisea; Sclerotium rolfsii; Fusarium solani; Alternaria alternata; Ganoderma sp.) of crops and multipurpose tree species. The whole genome sequence analysis was performed to unveil the genetic potential of these bacteria for plant protection. The complete genomes of PBs 12 and PBl 36 consist of a single circular chromosome with a size of 4.02 and 4.33 Mb and 4,171 and 4,606 genes, with a G + C content of 43.68 and 45.83%, respectively. Comparative Average Nucleotide Identity (ANI) analysis revealed a close similarity of PBs 12 and PBl 36 with other beneficial strains of B. subtilis and B. paralicheniformis and found distant from B. altitudinis, B. amyloliquefaciens, and B. thuringiensis. Functional annotation revealed a majority of pathway classes of PBs 12 (30) and PBl 36 (29) involved in the biosynthesis of secondary metabolites, polyketides, and non-ribosomal peptides, followed by xenobiotic biodegradation and metabolism (21). Furthermore, 14 genomic regions of PBs 12 and 15 of PBl 36 associated with the synthesis of RiPP (Ribosomally synthesized and post-translationally modified peptides), terpenes, cyclic dipeptides (CDPs), type III polyketide synthases (T3PKSs), sactipeptides, lanthipeptides, siderophores, NRPS (Non-Ribosomal Peptide Synthetase), NRP-metallophone, etc. It was discovered that these areas contain between 25,458 and 33,000 secondary metabolite-coding MiBiG clusters which code for a wide range of products, such as antibiotics. The PCR-based screening for the presence of antimicrobial peptide (cyclic lipopeptide) genes in PBs 12 and 36 confirmed their broad-spectrum antifungal potential with the presence of spoVG, bacA, and srfAA AMP genes, which encode antimicrobial compounds such as subtilin, bacylisin, and surfactin.

CONCLUSION

The combined in vitro studies and genome analysis highlighted the antifungal potential of pearl millet panicle-associated Bacillus subtilis PBs12 and Bacillus paralicheniformis PBl36. The genetic ability to synthesize several antimicrobial compounds indicated the industrial value of PBs 12 and PBl 36, which shed light on further studies to establish their action as a biostimulant for crop protection.