Streptomyces botrytidirepellens sp. nov., a novel actinomycete with antifungal activity against Botrytis cinerea

Streptomyces lycopersici sp. nov. and Streptomyces cucumeris sp. nov., two novel actinobacteria isolated from rhizosphere soil with broad-spectrum antifungal activity

Two actinobacterial strains, designated NEAU-383T and NEAU-Y11T, exhibiting antifungal activity, were isolated from the rhizosphere soil of plants in Harbin, Heilongjiang Province, and Guangzhou, Guangdong Province, respectively. Both strains formed short, wrinkled, spiral spore chains on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains NEAU-383T and NEAU-Y11T were most closely related to Streptomyces iranensis HM 35T, Streptomyces rapamycinicus NRRL B-5491T and Streptomyces coffeae CA1R205T. However, digital DNA-DNA hybridization values between the two strains and their close relatives (27.1% between the two strains; 27.5-59.0% for NEAU-383T; 27.0-39.8% for NEAU-Y11T) fell below the 70% species delineation threshold. The genomic G+C contents were 71.0 mol% for NEAU-383T and 70.5 mol% for NEAU-Y11T. Both strains contained glucose and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H6) and MK-9(H8), with NEAU-Y11T additionally containing MK-9(H4). The major fatty acids (>10%) in both strains included iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, whilst iso-C17 : 0 was also a major component in NEAU-383T. Both strains contained phosphatidylethanolamine and hydroxy-phosphatidylethanolamine as polar lipids. Additionally, NEAU-383T also possessed diphosphatidylglycerol, phosphatidylinositol, an unidentified ninhydride-positive lipid and five unidentified lipids, whereas NEAU-Y11T additionally contained two unidentified ninhydride-positive lipids and five unidentified lipids. Genomic analysis revealed that both strains possess abundant secondary metabolite biosynthesis gene clusters, including those for antibiotics, siderophores, polyketides and terpenoids, along with metabolic pathways associated with environmental adaptation. These findings provide insight into the potent antimicrobial activity exhibited by both strains. Based on genotypic, phenotypic and chemotaxonomic analyses, strains NEAU-383T and NEAU-Y11T represent two novel species within the genus Streptomyces, for which the names Streptomyces lycopersici (type strain NEAU-383T=JCM 36736T=MCCC 1K08878T) and Streptomyces cucumeris (type strain NEAU-Y11T=JCM 36418T=MCCC 1K08681T) are proposed.

Genomic Characterization and Establishment of a Genetic Manipulation System for Trichoderma sp. (Harzianum Clade) LZ117

Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction.

Bacillus velezensis SYL-3 suppresses Alternaria alternata and tobacco mosaic virus infecting Nicotiana tabacum by regulating the phyllosphere microbial community

The occurrence of plant diseases is closely associated with the imbalance of plant tissue microecological environment. The regulation of the phyllosphere microbial communities has become a new and alternative approach to the biological control of foliar diseases. In this study, Bacillus velezensis SYL-3 isolated from Luzhou exhibited an effective inhibitory effect against Alternaria alternata and tobacco mosaic virus (TMV). The analysis of phyllosphere microbiome by PacBio sequencing indicated that SYL-3 treatment significantly altered fungal and bacterial communities on the leaves of Nicotiana tabacum plants and reduced the disease index caused by A. alternata and TMV. Specifically, the abundance of P. seudomo, Sphingomonas, Massilia, and Cladosporium in the SYL-3 treatment group increased by 19.00, 9.49, 3.34, and 12.29%, respectively, while the abundances of Pantoea, Enterobacter, Sampaiozyma, and Rachicladosporium were reduced. Moreover, the abundance of beneficial bacteria, such as Pseudomonas and Sphingomonas, was negatively correlated with the disease indexes of A. alternata and TMV. The PICRUSt data also predicted the composition of functional genes, with significant differences being apparent between SYL-3 and the control treatment group. Further functional analysis of the microbiome also showed that SYL-3 may induce host disease resistance by motivating host defense-related pathways. These results collectively indicate that SYL-3 may suppress disease progression caused by A. alternata or TMV by improving the microbial community composition on tobacco leaves.