Streptomyces alfalfa strain 11F has inhibitory effects on many phytopathogenic fungi and improves the establishment and biomass yield of switchgrass. However, the antagonistic effects of strain 11F on Fusarium wilt of watermelon and its secondary metabolites that contribute to its biocontrol activity are poorly understood. We evaluated the antagonistic and growth-promoting effects of strain 11F and conducted a transcriptome analysis to identify the metabolites contributing to antifungal activity. Strain 11F had marked inhibitory effects on six fungal pathogens. The incidence of Fusarium wilt of watermelon seedlings was decreased by 46.02%, while watermelon seedling growth was promoted, as indicated by plant height (8.7%), fresh weight (23.1%), and dry weight (60.0%). Clean RNA-sequencing data were annotated with 7553 functional genes. The 2582 differentially expressed genes (DEGs) detected in the Control vs. Case 2 comparison were divided into 42 subcategories of the biological process, cellular component, and molecular function Gene Ontology categories. Seven hundred and forty functional genes (55.47% of the DEGs) were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways, reflecting the complexity of the strain 11F metabolic regulatory system. The expression level of the gene phzF, which encodes an enzyme essential for phenazine-1-carboxylic acid (PCA) synthesis, was downregulated 3.7-fold between the 24 h and 48 h fermentation time points, suggesting that strain 11F can produce phenazine compounds. A phenazine compound from 11F was isolated and identified as phenazine-1-carboxamide (PCN), which contributed to the antagonistic activity against Fusarium oxysporum f. sp. niveum. PCA was speculated to be the synthetic precursor of PCN. The downregulation in phzF expression might be associated with the decrease in PCA accumulation and the increase in PCN synthesis in strain 11F from 24 to 48 h. Streptomyces alfalfae 11F protects watermelon seedlings from Fusarium wilt of watermelon and promotes seedling growth. The transcriptome analysis of strain 11F provides insights into the synthesis of PCN, which has antifungal activity against F. oxysporum f. sp. niveum of watermelon.

Collimonas species are soil bacteria characterised by their ability to attach to and utilise fungi as a food source (mycophagy), as well as their chitin-degrading capacity (via chitinase production). These attributes, alongside volatile compounds, are thought to contribute to their function as fungal antagonists, including economically important plant pathogens. Despite this, studies have found no relationship between antifungal activity and chitinase production, or volatile compounds in Collimonas pratensis isolate ZL261, and there have been no studies on genetic control and regulatory biosynthesis of antifungal substances in Collimonas species. In this study, we showed that low concentrations of dissolved oxygen were unfavourable for growth and antifungal activity. We successfully introduced the gene vgb encoding Vitreoscilla haemoglobin (VHb) into isolate ZL261. The heterologous expression of VHb not only enhanced cell growth, but also improved antifungal activity against the brown rot fungus Monilinia fructicola under oxygen-restricted conditions; 18.6% of untreated peach fruits were infected (average lesion diameter: 9.2 mm), while only 10.8% of fruit treated with the transformed isolate, ZV261, were infected (average lesion diameter: 5.4 mm). These results suggest that the antagonism have been due to the secreted secondary metabolites, which are sensitive to the oxygen-restricted conditions.

Setaria viridis (L.) Beauv. is rapidly emerging as a model plant within the Panicoideae subfamily of Poaceae for studying C4 photosynthesis. The ‘Fangshan’ ecotype of S. viridis exhibits high adaptability to drought and nutrient-poor environments and holds historical significance in traditional Chinese medicine. Nevertheless, cytoplasmic genomic resources for this species, particularly its mitochondrial genome, remain entirely uncharacterized. To address this gap, we assembled the complete mitochondrial genome of the ‘Fangshan’ ecotype de novo using a hybrid approach combining Oxford Nanopore long reads and Illumina short reads. The mitochondrial genome adopts a predominantly single circular conformation with a total length of 437, 906 bp and a GC content of 43.96%, containing 33 unique protein-coding genes, 20 tRNA genes, and 3 rRNA genes. Furthermore, 111 Simple Sequence Repeats (SSRs), 33 tandem repeats, and 493 pairs of dispersed repeats were identified. Analysis revealed 31 plastid-derived DNA sequences integrated into the mitochondrial genome, constituting 3.19% of its total length. These sequences include one protein-coding gene and nine tRNA genes. Phylogenetic reconstruction demonstrated that the S. viridis clusters closely with S. italica , and Poaceae species form a distinct clade. Subsequently, in silico prediction identified 463 potential RNA editing sites (exclusively C-to-U conversions) across the 33 mitochondrial protein-coding genes. ccmC , ccmFN , and nad2 carried the highest numbers of predicted editing sites (36, 30, and 30, respectively). As core components of the mitochondrial electron transport chain, extensive editing in these genes may reflect strong functional constraints essential for energy metabolism during foxtail millet domestication. This study establishes a foundational genomic resource for investigating cytoplasmic genome evolution and the genetic basis of environmental adaptation in the genus Setaria .