TL;DR
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.
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.
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 ).
Genome analysis identified genetic features potentially associated with stress adaptation and iron/tryptophan metabolism, providing additional ecological context for this plant-associated isolate.
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.
Abstract Two alphaproteobacterial strains, designated EGI L300112T and EGI L300120, were isolated from sediment collected from Chaiwopu Lake in Xinjiang, China. The taxonomic position of the two strains was determined using polyphasic taxonomic analysis and phylogenomic analysis. Based on 16S rRNA gene sequence similarities, strain EGI L300112T and EGI L300120 were both closely related to Pelagerythrobacter rhizovicinus AY-3RT and shared the highest sequence identities of 96.2% and 96.3%, respectively. However, phylogenetic analysis based on the 16S rRNA gene and genomes clearly demonstrated that the two strains formed a distinct clade with validly published species of the genus Altererythrobacter. Furthermore, the two strains exhibited distinct phenotypic, physiological and genotypic characteristics that differentiate them from other related type species of the genus Altererythrobacter and related species in the family Erythrobacteraceae. Cells of the two strains were aerobic, Gram-stain negative, non-motile and rod-shaped. Optimal growth conditions for EGI L300112T and EGI L300120 occurred on marine agar 2216 at pH 7 at 30 °C. The major respiratory quinone was Q-10. The detected polar lipids of two strains included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and unidentified phospholipids. The major fatty acids (>10%) were identified as summed feature 3 (C16 : 1ω7 c/C16 : 1ω6 c) and summed feature 8 (C18 : 1ω7 c). The G+C content of strain EGI L300112T and EGI L300120 was 61.2% and 61.4%, respectively. Based on differential phenotypic and genotypic characteristics of the two strains and related species in the genus Altererythrobacter, the two strains should be classified as representing a new species of this genus, for which the name Altererythrobacter chaiwopuensis sp. nov. is proposed. The type strain is EGI L300112T (=MCCC 1K09432T=KCTC 8712T).
On the basis of evidence presented in this study, strain BYT-45T represents a novel species of the genus Shinella, for which the name Shinella agrisoli sp.
