- Volume 75, Issue 6, 2025

Three slow-growing rhizobial strains, designated as 1AS2LT, 1AS20L and 1AS5L, were isolated from nodules of Acacia saligna in Borj Cedria, northern Tunisia. These strains, which belong to the symbiovar cyanophyllae, were characterized using a polyphasic approach. Phylogenetic analysis of the 16S rRNA (rrs) gene placed these strains within the genus Bradyrhizobium, specifically in the superclade associated with Bradyrhizobium japonicum. Further phylogenetic analysis using concatenated sequences of the recA, atpD, glnII and gyrB genes (totalling 1,734 bp) positioned the strains in a distinct lineage, with Bradyrhizobium shewense identified as their closest related species, sharing a sequence identity of 95.2%. The type strain, 1AS2LT, exhibited average nucleotide identity values of 89.10%, 89.08% and 89.00% with the type strains of the closest valid species: Bradyrhizobium frederickii, B. shewense and Bradyrhizobium ottawaense, respectively. Additionally, digital DNA–DNA hybridization values confirmed the novelty of strain 1AS2LT, showing low similarity (38.0%–38.3%) with the type strains of the closest known species. Phylogenomic analyses based on up-to-date bacterial core genes, Type (Strain) Genome Server and the Genome Taxonomy Database (GTDB) pipelines further supported the uniqueness of the 1AS2LT, 1AS20L and 1AS5L strains. The GTDB analysis also robustly clustered two strains (SZCCT0449 and NSD-1) with our strains, suggesting putative members of the proposed novel species. The differentiation of these novel strains from their closest phylogenetic neighbours was also corroborated by phenotypic, physiological and fatty acid content analyses. Based on genomic, phenotypic and biochemical data, we propose the establishment of a novel species, Bradyrhizobium tunisiense sp. nov., with strain 1AS2LT (=LMG 33170T=DSM 114401T) as the type strain.

An erratum of this article has been published full details can be found at 10.1099/ijsem.0.006854

A novel Gram-negative, oxidase- and catalase-positive, rod-shaped bacterium, designated strain KX21116T, was isolated from the mussel Gigantidas platifrons collected from a cold seep field in the South China Sea. Strain KX21116T grew optimally at 28 °C, pH 6.0 with 3% (w/v) NaCl, under aerobic and microaerobic conditions. Its genome size was 3.16 Mb, with a G+C content of 28.4 mol%. The 16S rRNA sequences revealed that strain KX21116T was closely related to Arcobacter nitrofigilis DSM 7299T (98.77% gene sequence similarity) and Arcobacter acticola AR-13T (95.58%). Phylogenetic and phylogenomic analysis revealed that strain KX21116T clustered with the type species of the genus Arcobacter, with A. nitrofigilis DSM 7299T as its nearest neighbour. The genomic average nucleotide identity (orthoANI) values between strain KX21116T and A. nitrofigilis DSM 7299T were 92.74%, while the in silico DNA–DNA hybridization (GGDC) values of the two strains were 48.8%. The predominant fatty acids are C16:0, C16:1  ω7c/C16:1  ω6c and C18:1  ω7c/C18:1  ω6c. Based on a comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX21116T represents a novel species of the genus Arcobacter, for which the name Arcobacter iocasae sp. nov. is proposed. The type strain is KX21116T (=MCCC 1K08505T=KCTC 92900T=JCM 35939T).

The genus Moraxella (Moraxellaceae, Pseudomonadales) comprises a diverse group of bacteria inhabiting human and animal mucosa, as well as environmental niches such as water, soil and food. While some species are clinically significant pathogens, others play ecological or biotechnological roles. Despite previous taxonomic revisions, Moraxella remains polyphyletic, necessitating a refined classification. In this study, we conducted comprehensive taxogenomic analyses integrating core protein phylogeny, average amino acid identity and the percentage of conserved proteins, along with 16S rRNA similarities and inferred phylogeny. Our results revealed three distinct phylogenetic clusters within Moraxella. The core group, comprising Moraxella lacunata NBRC 102154T and closely related species, exhibited strong genomic cohesion. A second cluster, consisting of Moraxella boevrei DSM 14165T, Moraxella osloensis CCUG 350T and Moraxella atlantae NBRC 14588T, showed greater genetic affinity to Faucicola mancuniensis GVCNT2T, supporting their reassignment to the genus Faucicola. The third group, represented by Moraxella lincolnii CCUG 9405T, was phylogenetically distinct, occupying a basal position relative to Psychrobacter, indicating the need for its classification within a novel genus within the family Moraxellaceae, for which we propose the name Lwoffella lincolnii gen. nov., comb. nov. Phenotypic data compiled from the original published descriptions of the respective species, including fatty acid composition and enzymatic profiles, further corroborated these genomic findings. This study refines Moraxella taxonomy by clarifying genus boundaries and evolutionary relationships, with implications for ecology and clinical microbiology.

Species clustering within Dickeya zeae has been recently identified as complex, encompassing validly published names, including Dickeya oryzae and Dickeya parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93 to 99.9% and 91.8 to 99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae and D. oryzae ranged from 94.4–95.9% to 57.2–66.5%, respectively. These values fall below the proposed boundaries for species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis of ten housekeeping genes, whole genome and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the 7 pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological and phylogenomic analyses, we propose the reclassification into a new species of the five pineapple strains from Hawaii A5391, A5410T, A5611, A6136 and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananatis sp. nov. for this taxon, represented by the type strain A5410T (=ICMP 25020T=LMG 33197T).

A novel chitinolytic bacterium, designated as NN19T, was isolated from the intertidal mudflat in Leizhou, Guangdong Province, PR China, and subjected to polyphasic taxonomy studies. Strain NN19T is a Gram-negative short rod-shaped bacterium that is motile via a single polar flagellum. Growth occurred at temperatures of 15 °C and 37 °C (optimal 30 °C), pH 6.5–8.0 (optimal pH 7.0) and sodium chloride concentration of 0%–3% (optimal 0.5%–1%). It was identified as a Cellvibrio species based on the results of 16S rRNA gene sequence analysis, and it showed the highest degree of sequence similarity with Cellvibrio fontiphilus MVW-40T (97.87%). The main fatty acids of NN19T were found to be summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and C18 : 1  ω7c. The polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The respiratory quinone was shown to be ubiquinone-8. Strain NN19T had a genome of 4.46 Mb with a G+C content of 47.82%. The average nucleotide identity and digital DNA–DNA hybridization value between strain NN19T and C. fontiphilus MVW-40T are 75.47% and 20.4%, respectively. Based on phylogenetic analysis and phenotypic data, we concluded that strain NN19T represents a novel species belonging to the genus Cellvibrio, for which the name Cellvibrio chitinivorans sp. nov. is proposed. The type strain is NN19T (=MCCC 1K08847T=KCTC 8393T).

Conidiobolus coronatus (Cost.) Batko is the most common species within the genus Conidiobolus sensu stricto (s.s.). Historically, the presence of villose conidia in C. coronatus was considered a unique morphological characteristic distinguishing it from other Conidiobolus s.s. members. However, Conidiobolus lunulus, reported to infect leafcutter ants and produce half-moon-shaped microspores, was identified as the second species with villose conidia. These findings suggest that C. coronatus represents a species complex. In the present study, we isolated the third species with villose conidia, characterized by its long villi and named it Conidiobolus longivillosus sp. nov. Phylogenetic analyses based on single-gene phylogenies (nucLSU, nucSSU and ITS) and multi-gene phylogenies (nucLSU, nucSSU, TEF1, ITS and mtSSU), along with the pairwise homoplasy index test and Poisson tree processes analysis, were performed to recognize this cryptic species. The results not only support C. longivillosus as an independent species but also imply the existence of cryptic species within the C. coronatus species complex.

Two red yeast strains, NYNU 232201 and NYNU 232218, were isolated from the phylloplane of Pinus massoniana and Cinnamomum camphora, respectively, in Sifangjing Village, Pingtang County, Guizhou Province, China. Molecular phylogenetic analyses placed these strains in close relation to Symmetrospora clarorosea, Symmetrospora gracilis and Symmetrospora eucalyti. Genetically, the isolates differed from the type strains of these related species by seven to nine base substitutions (1.2–1.5%) in the D1/D2 domain and by more than 15 base mismatches (2.6%) in the internal transcribed spacer region. Phenotypically, the two strains can be distinguished from S. clarorosea and S. gracilis by their ability to assimilate d-glucosamine and grow at 30 °C, as well as their inability to assimilate ribitol. Physiological data for S. eucalypti were not available for comparison. No sexual morph was observed in either strain. Based on molecular and phenotypic differentiation, the novel yeast species Symmetrospora pini sp. nov. is proposed with holotype CICC 33601T (MycoBank MB 857729).

Two basidiomycete yeast strains, designated as 21S12 and 12S11, were isolated from the flowers of Yulania denudata collected from the Beijing Olympic Forest Park, PR China. Molecular phylogenetic analyses based on the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer (ITS) region revealed that these strains represent a novel species within the genus Fonsecazyma. The new species, Fonsecazyma yulaniae sp. nov., is most closely related to Fonsecazyma mujuensis CBS 10308T, with sequence divergences of 4.3% (28 substitutions and 2 indels) in the D1/D2 domain and 8.4% (28 substitutions and 10 indels) in the ITS region. Phenotypically, F. yulaniae sp. nov. differs from F. mujuensis CBS 10308T in its ability to assimilate inulin and creatinine, as well as its inability to assimilate lactose and erythritol. Additionally, F. yulaniae sp. nov. can grow in a vitamin-free medium and in a medium supplemented with 50% glucose, conditions under which F. mujuensis cannot grow. The holotype of F. yulaniae sp. nov. is CGMCC2.5852T, and its taxonomic description has been registered in Fungal Names (FN572294) and in Mycobank (MBT10026390).