Combining phylogenomic, virulence, phenotypic, and pathogenic data, Pectobacterium nicotianae sp.
Abstract
Five Gram-negative, facultatively anaerobic bacteria were isolated from the hollow stalk tissues of tobacco plants in Yunnan, China. Based on polyphasic taxonomic data, they were identified as a new Pectobacterium species. Phylogenetic analyses of 16S rRNA and the concatenated dnaX-leuS-recA genes grouped them into a distinct monophyletic clade. Genome analyses showed high average nucleotide identity (ANIb 96.96–97.63%) and digital DNA-DNA hybridization (dDDH 76.2–80.1%) values, supporting their classification as a single species. However, three indices, including lower dDDH (67.9%), borderline ANIb (95.89%), and phylogenomic separation with 99% support, differentiate them from Pectobacterium brasiliense IPO 3540T. Comparative genomics across 24 reference strains revealed differences in virulence factors and specific plant cell wall-degrading enzyme profiles, highlighting adaptations to different hosts. Biochemical tests showed that all isolates lacked β-glucosidase and exhibited unique carbon utilization patterns; chemotaxonomically, strain 21LCBS03T produced only menaquinone MK-8. Pathogenicity experiments confirmed that four strains caused severe soft rot and hypersensitive responses on various hosts, while strain BSHS4, with a dDDH of 76.2% relative to 21LCBS03T, showed reduced virulence—possibly a subspecies. Reanalysis of 633 Pectobacterium genomes from NCBI reclassified 121 strains into this new species, exposed common misidentifications, and identified 9 candidate novel species awaiting phenotypic validation. Combining phylogenomic, virulence, phenotypic, and pathogenic data, we propose Pectobacterium nicotianae sp. nov., with 21LCBS03T (=GDMCC 1.3317T = CCTCC AB2022131T = JCM 35650T) designated as the type strain.
Members of the phylum
Actinomycetota
are widely distributed across diverse environments and are well known for their metabolic versatility and capacity to produce bioactive compounds. In this study, strain ZE1316R2Aᵀ was isolated from the saline water collected from Lake Zima (Morocco) and subjected to comprehensive polyphasic taxonomic characterisation. Phylogenetic analysis based on the 16 S rRNA gene placed strain ZE1316R2Aᵀ within the genus
Streptomyces
, showing highest sequence similarity with
S. albidoflavus
DSM 40,455
T
(99.71%). However, genome-based indices, including average nucleotide identity (ANIb = 94.84%, ANIm = 96.09%) and digital DNA-DNA hybridization (dDDH = 64.9%), supported its distinction as a separate species. The draft genome (7.41 Mb; G + C = 73.26 mol%) comprises 6,464 coding sequences and reveals the presence of strain-specific genomic regions and biosynthetic gene clusters. Comparative analyses highlighted both a conserved core genome and a substantial accessory genome component, reflecting genomic differentiation relative to closely related taxa. Phenotypic and chemotaxonomic characteristics were consistent with assignment to the genus
Streptomyces
, while supporting its differentiation at the species level. Based on the combined genomic, phenotypic, and chemotaxonomic evidence, strain ZE1316R2Aᵀ represents a novel species of the genus
Streptomyces
, for which the name
Streptomyces zimensis
sp. nov., is proposed. This study expands current knowledge of
Streptomyces
diversity associated with saline environments and highlights the genomic diversity present within closely related taxa. The type strain is ZE1316R2Aᵀ (= CCMM B1331
T
= DSM 120541
T
).
E. Oubassou, Soukaina Oudchaira, V. Cognat et al.· Annals of Microbiology· 0 citations
Genomic interrogation revealed conservation of energy metabolism pathways typical of rhizobia; however, comparative genomic analyses revealed that genes associated with both nitrogen fixation and denitrification are uniquely conserved in the genome of Phyllobacterium sp.
Hironaga Akita, Y. Itoiri, Y. Shinto et al.· Current Microbiology· 0 citations
A novel bacterial strain, CR191T, was isolated from maize (Zea mays) rhizosphere soil. The strain is Gram-stain-negative, oxidase-positive, rod-shaped, non-motile, and aerobic. Phylogenetic analysis based on 16S rRNA gene sequences placed CR191T within the genus Dyella, with highest similarity to Dyella flava DHOC52T (98.23%) and Dyella dinghuensis DHOA06T (98.16%). The genomic DNA G+C content was 66.19%. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CR191T and the type strains of the other 36 validly published Dyella species ranged from 79.0 to 86.6% and 20.2–28.7%, respectively, both below the recognized thresholds for species delineation. Genome mining identified several putative biosynthetic gene clusters showing similarity to known clusters associated with diverse secondary metabolites, including saframycin, cosmomycin, and malleobactin biosynthesis. The major cellular fatty acids were iso-C17:0, iso-C15:0, and summed feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl). The polar lipid profile comprised phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and two unidentified polar lipids; the sole respiratory quinone was ubiquinone Q-8. Based on a combination of phenotypic, chemotaxonomic, genomic, and phylogenetic characteristics, strain CR191T is considered to represent a novel species of the genus Dyella, for which the name Dyella cornirhiza sp. nov. is proposed. The type strain is CR191T (=CCAM 2032T = JCM 36807T).
It is confirmed that strain C159T is a novel multifunctional rhizobacterium for the biocontrol of tomato bacterial wilt and represents a novel species in the genus Pseudoneobacillus sp.
Shengfeng Pan, Zengwei Feng, Meng Chen et al.· International Journal of Sys...· 0 citations
Bacterial strains were isolated from different locations and screened for plant growth promoting (PGP) features. Comparative analyses of the 16S gene sequences of 5 of the strains indicated taxonomic relatedness within the genus Paenibacillus. A polyphasic taxonomic approach was employed to study the strains in detail to clarify their phylogenetic position. Genome-based analyses, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), revealed values consistently below the accepted species delineation thresholds when compared with closest relatives of each strain. Additionally, the strains showed clear differences in their physiological and biochemical profiles to the type strains of the closest related species. A notably diverse set of genes potentially involved in plant growth promotion was detected in all strains. With respect to the analyses reported here, the following new names are proposed: Paenibacillus corni sp. nov., with AK-167T as the type strain (= LMG 34403T = DSM 121689T); Paenibacillus vaccinii sp. nov., with AK-264T as the type strain (= LMG 34404T = DSM 121714T); Paenibacillus ericacearum sp. nov., with AK-265T as the type strain (= CCM 6913T = LMG 34405T = DSM 121715T); Paenibacillus polytrichii sp. nov., with AK-286T as the type strain (= CCM 9614T = LMG 34406T = DSM 121716T); and Paenibacillus artemisiae sp. nov., with DT-106T as the type strain (= LMG 34409T = CCM 9610T = DSM 121690T).
P. Kämpfer, A. Lipski, Kathy S. Lawrence et al.· Systematic and Applied Micro...· 0 citations
Findings establish B. velezensis strains BP5 and BP103 as highly promising biocontrol agents, combining high genetic stability with diverse secondary metabolite profiles, suitable for development into sustainable microbial bio-bactericides.
Lê Uyển Thanh, Vu Nhat Tan, T. Huyen et al.· Frontiers in Microbiology· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
