Three actinobacterial strains, AW10-10T, M8-1T and HGHZ1-2T, were isolated from soil in Yunnan Province, China. Analyses of 16S rRNA gene sequences and shotgun-sequenced draft genomes placed them within the genus Microbacterium. OrthoANI, FastANI and dDDH values between the three strains and their closest relatives were 75.7–79.6%, 79.9–81.9% and 19.7–22.5%, respectively, all well below the accepted species-level thresholds. Cells of all three strains were Gram-stain-positive, aerobic and rod-shaped. The major fatty acids were anteiso-C17:0, anteiso-C15:0 and iso-C16:0 in AW10-10T and HGHZ1-2T, and anteiso-C15:0, anteiso-C17:0 and iso-C16:0 in M8-1T. AW10-10T and M8-1T contained ribose, galactose, mannose, glucose and minor rhamnose, whereas HGHZ1-2T lacked rhamnose. The predominant menaquinones were MK-12 and MK-13 in AW10-10T, MK-13 and MK-12 in HGHZ1-2T, and MK-10, MK-11 and MK-9 in M8-1T. Polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in AW10-10T and HGHZ1-2T, but two unidentified glycolipids in M8-1T. DNA G + C contents were 70.0, 69.7 and 69.5 mol%, respectively. The strains represent three novel species, Microbacterium altimontanum sp. nov., Microbacterium longlingense sp. nov. and Microbacterium cucumeris sp. nov., with type strains AW10-10T (=GDMCC 16749T = KCTC 59693T), M8-1T (=GDMCC 16752T = KCTC 59696T) and HGHZ1-2T (=GDMCC 16751T = KCTC 59694T), respectively.
Wenqi Lai, Xiankun Zhang, Z. Duan et al.· Microorganisms· 0 citations
Three Gram-stain-positive, aerobic, non-motile, rod-shaped bacterial strains, designated LJC-15T, NGA-4T and QZ2-6-4T, were isolated from the rhizosphere soils of Capsicum, Cucurbita and Solanum melongena, respectively, in Yunnan Province, China. Phylogenetic and phylogenomic analyses placed the three strains within the genus Agromyces but distinguished them from recognized species. All ANI and dDDH values between the novel strains and phylogenetically related type strains were well below the generally accepted species delineation thresholds. The three strains could also be differentiated from selected reference type strains by phenotypic characteristics. Chemotaxonomically, they contained MK-12 as the predominant menaquinone and anteiso-C15:0, anteiso-C17:0 and iso-C16:0 as the major fatty acids, while their whole-cell sugar and polar lipid profiles were consistent with those characteristic of the genus Agromyces. On the basis of the combined phylogenetic, genomic, phenotypic and chemotaxonomic evidence, strains LJC-15T, NGA-4T and QZ2-6-4T are proposed to represent three novel species of the genus Agromyces, for which the names Agromyces capsici sp. nov., Agromyces cucurbitae sp. nov. and Agromyces solani sp. nov. are proposed, respectively. The type strains are LJC-15T (=GDMCC 1.6754T = KCTC 59690T), NGA-4T (=GDMCC 1.6755T = KCTC 59691T) and QZ2-6-4T (=GDMCC 1.6756T = KCTC 59692T), respectively.
Z. Duan, Shuailiang Shi, Bang-Li Huang et al.· Microorganisms· 0 citations
Abstract Colletotrichum spp. are widespread fungal pathogens that cause anthracnose in numerous economically important crops and, exhibiting extensive taxonomic, host plant, and lifestyle diversity. Here, we analyzed the genome sequences of 150 strains representing 97 species across 15 species complexes and four singletons, including and integrating both newly assembled and publicly available genomes. Phylogenomic investigation clarified the taxonomy of Colletotrichum and resolved misidentifications. We identified variations in genome architecture contributed by phylogenetic lineages, host types, and lifestyles, with transposable element proliferation playing significant roles. Interestingly, codon usage bias followed phylogenetic patterns, with species complexes forming distinct clusters and exhibiting a significant bistable co-evolutionary relationship with tRNA genes. Functional gene repertoires displayed coordinated shifts, with higher abundance in broad host-range species complexes and in strains associated with woody or dicotyledonous hosts. Although most functional categories retained strong phylogenetic signals, co-occurrence analysis of weak-signal categories identified modules related to host cell wall disruption, fungal cell wall remodeling, and virulence that were significantly associated with ecological differentiation. Evolutionary trajectories and gene family dynamics further revealed divergent ecological strategies, with oxidative versus rapid-response detoxification in woody- and herbaceous-associated lineages, respectively. The diversifications were accompanied by woody-specific expansion of GH39 and alkaline proteases and progressive differentiation of pectin-degrading capacity, including contraction in woody lineages and divergence between dicot- and monocot-associated herbaceous lineages. The C. gloeosporioides species complex emerged with a comprehensive expansion of detoxification and cell wall-degrading capacities, likely contributing to its broad host range. In contrast, endophytic lineages exhibited convergent gene family contraction in adhesion and cell wall remodeling. Together, this study revealed concordance of codon usage and functional gene abundance with phylogeny, along with diverse host- and lifestyle-associated adaptive strategies in this important group of plant pathogens.
Jian-Xin Shen, M. Qiao, Jiahao Hong et al.· IMA Fungus· 0 citations