International Journal of Systematic and Evolutionary Microbiology - Current Issue

An actinobacterial strain, designated DW29H23T, was isolated from greater duckweed Spirodela polyrhiza. The strain was investigated using a polyphasic taxonomy approach. The comparison of the 16S rRNA gene sequence showed that strain DW29H23T was most closely related to Mumia xiangluensis NEAU-KD1T (99.2%) and Mumia quercus NEAU-365T (98.9%). The average nucleotide identity and digital DNA–DNA hybridization values between the strain and closest type strains were below the threshold for species delineation. The strain was Gram-stain-positive, non-spore-forming and non-motile. Cells were irregular, rod-shaped. The whole-cell hydrolysates contained ll -diaminopimelic acid. The whole-cell sugars were glucose and ribose. The polar lipid profiles contained diphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The major cellular fatty acids (>10%) were C16:0, 10-methyl-C18:0 and C18:1  ω9c. The major menaquinone was MK-9(H4). The G+C content was 71.7%. Genotypic, phenotypic and chemotaxonomic characterizations of strain DW29H23T demonstrated that the strain represents a novel species of the genus Mumia, for which the name Mumia spirodelae sp. nov. is proposed. The type strain is DW29H23T (=TBRC 18998T=NBRC 116930T).

Two bacterial strains, YIM 151858-1T and YIM 151500-1T, were isolated from soil samples collected on Weizhou Island, Beibu Gulf, South China Sea, China. Both strains were aerobic, Gram-negative, non-flagellated and rod-shaped bacteria. Phylogenetic analyses based on the 16S rRNA gene sequences showed that both strains belonged to the genus Hymenobacter of the family Hymenobacteraceae. Strains YIM 151858-1T and YIM 151500-1T exhibited 16S rRNA gene sequence similarities of 96.04% and 95.29% to Hymenobacter deserti and Hymenobacter rubripertinctus, respectively. In strain YIM 151858-1T, the major cellular fatty acids (>10%) were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C17 : 0 3-OH, whereas the detected polar lipids included phosphatidylethanolamine (PE), unidentified aminophospholipids (APL), unidentified phospholipids and unidentified lipid (L). In strain YIM 151500-1T, the major cellular fatty acids (>10%) were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and anteiso-C15 :  0. The detected polar lipids included unidentified aminolipids, PE, APL and L. The predominant isoprenoid quinone in both strains was MK-7. Based on their genome sequences, the G+C content of both strains YIM 151858-1T and YIM 151500-1T was 61.5 mol%. Compared with the most closely related species H. deserti ZLB-3T and H. rubripertinctus KCTC 62163T, the strains YIM 151858-1T and YIM 151500-1T had 75.4% average nucleotide identity, 68.8% average amino acid identity and 21% digital DNA–DNA hybridization value average, which were below the thresholds for delineation of the two novel species. Based on the results of the polyphasic taxonomy, we propose that strains YIM 151858-1T and YIM151500-1T represent novel species, for which we propose the names Hymenobacter latericus sp. nov. (type strain YIM 151858-1T=MCCC 1K8320=KCTC 92732) and Hymenobacter weizhouensis sp. nov. (type strain YIM 151500-1T=MCCC 1K08054=KCTC 92531) within the genus Hymenobacter.

Four strains (LJ668T/LJ756 and CY350T/CY353) belonging to the genus Chryseobacterium were isolated from the Qinghai–Tibet Plateau soils. Cells were aerobic, Gram-stain-negative, rod-shaped, yellow-pigmented, non-motile and non-spore-forming. According to the 16S rRNA gene sequence alignment, the strain pair LJ668T/LJ756 shared the highest similarities to Chryseobacterium aahli T68T (98.09%) and Chryseobacterium limigenitum SUR2T (98.09%), and the other one (CY350T/CY353) to Chryseobacterium aquaticum KCTC 12483T (97.98/98.13%). The phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that these four strains generated two separate clades in genus Chryseobacterium. The digital DNA–DNA hybridization and average nucleotide identity values of four novel isolates with other members of the genus Chryseobacterium were far below 70.0% and 95.0–96.0 % thresholds. The genomic DNA G+C content of LJ668T and CY350T is both 35.0 mol%. The major cellular fatty acids of the two pair strains are iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). MK-6 is the only respiratory quinone for strains LJ668T and CY350T. The polar lipids of strain LJ668T are phosphatidylethanolamine (PE), L1–5 and AL1–5, and the strain CY350T is PE, L1–4, AL1–2, diphosphatidylglycerol, phosphoglycolipid and GL1–3. According to the results of genotypic, phenotypic and biochemical analyses, these four strains represent two novel species of the genus Chryseobacterium, for which the names Chryseobacterium chendengshani sp. nov. and Chryseobacterium wangxinyae sp. nov. are proposed. The type strains are LJ668T (=CGMCC 1.17165T=JCM 33877T) and CY350T (=GDMCC 1.3790T=KCTC 25690T), respectively.

Strain P3-BQ1T is a Gram-negative, aerobic, non-spore-forming bacterium with gliding motility and filamentous cells. It was isolated in 2018 from the gills of a diseased Atlantic salmon (Salmo salar) during an outbreak of tenacibaculosis in a Chilean fish farm. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain P3-BQ1T belongs to the genus Tenacibaculum and is most closely related to Tenacibaculum dicentrarchi 35/09T (98.53%), ‘Tenacibaculum pacificus’ 18-2881-A (98.46%), Tenacibaculum aestuariivivum JDTF-79T (98.46%), Tenacibaculum finnmarkense TNO010 (97.85%) and Tenacibaculum piscium TNO20T (97.41%). The genome size of strain P3-BQ1T is 2,777,603 bp, with a DNA G+C content of 29.18 mol%. The strain has an OrthoANI score lower than 95% compared to the types of all validly named Tenacibaculum species, with the closest neighbour being T. dicentrarchi 35/09T (score 87.41 %). In contrast, P3-BQ1ᵀ and ‘T. pacificus’ 18-2881-A shared a 96.58%, thus exceeding the species threshold. This result is also supported by whole-genome in silico DNA–DNA hybridization/Genome-to-Genome Distance Calculator values, indicating that strains P3-BQ1T and 18-2881-A are conspecific. Strain P3-BQ1T contains MK-6 as its sole detectable menaquinone. The polar lipids profile includes glycolipids (n=2), aminolipids (n=3) and unidentified lipids (n=5). The predominant cellular fatty acids (>5 %) are C13 : 1, C15 : 0, iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1ω7с/C16 : 1ω6с). An immersion challenge was conducted to assess the pathogenic potential in Atlantic salmon. Our findings indicate that strain P3-BQ1T alone does not cause significant mortality, suggesting it is likely non-pathogenic to this species. Based on the phenotypic, phylogenetic and genotypic data presented, Tenacibaculum salmonis sp. nov. is proposed here with type strain P3-BQ1T (=IMI 507635T=RGM 3581T), being 18-2881-A an additional strain.

A thermophilic, strictly anaerobic, Gram-stain-negative and ferric iron-reducing bacterium, designated as DY30410T, was isolated from a hydrothermal sulphide sample collected from the Southwest Indian Ocean Ridge during the cruise DY30 of R/V Da Yang Yi Hao. Cells of strain DY30410T were rod-shaped with rounded ends and motile with one or more laterally inserted flagellum (flagella). Strain DY30410T grew optimally at pH 6.5–7.0, 50 °C, with salinity (sea salts) of 35–45 g l−1. Ferric oxyhydroxide, ferric chloride, thiosulphate and elemental sulphur can be used as electron acceptors. Glucose and starch are used for growth. Elemental sulphur or yeast extract is not necessary. The principal fatty acids of strain DY30410T were iso-C15:0, C16:0, 3OH-iso-C14:0 and anteiso-C15:0. No respiratory quinone was detected. Phylogenetically, strain DY30410T branched within the family Thermohalobacteraceae with Caloranaerobacter ferrireducens DY22619T being its closest phylogenetic relative (98.4% similarity), followed by the type species Caloranaerobacter azorensis MV1087T (97.2%). Strain DY30410T has a draft genome size of 2.57 Mbp and has 2,852 predicted coding sequences. The genome DNA G+C content of strain DY30410T was 29.2 mol%. The in silico DNA–DNA hybridization between strain DY30410T and its closest relatives, C. ferrireducens DY22619T or C. azorensis MV1087T, was all 45.5%. The average nucleotide identity values between strain DY30410T and C. ferrireducens DY22619T and C. azorensis MV1087T were 91.9 and 91.3%, respectively. Phylogenomic analysis also showed that strain DY30410T branched within the family Thermohalobacteraceae with C. ferrireducens DY22619T and C. azorensis MV1087T being its closest relatives. On the basis of phenotypic, phylogenetic and chemotaxonomic characteristics, we propose a representative of a new species in the genus Caloranaerobacter, for which the name Caloranaerobacter longqiensis sp. nov. is proposed. The type strain is DY30410T (=KCTC 25912T=MCCC 1A01531T).

The genus Apilactobacillus currently includes 12 species with validly published names, the majority of which are closely associated with honeybees. A Gram-positive, facultatively anaerobic, catalase-negative and fructose-dependent strain, designated 1-1-2T, was isolated from the gut of a honeybee (Apis mellifera). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1-1-2ᵀ represents a distinct lineage within the genus Apilactobacillus, with its closest phylogenetic neighbours being Apilactobacillus kunkeei YH-15T (99.8% sequence similarity), Apilactobacillus nanyangensis HN36-1T (99.8%) and Apilactobacillus apinorum Fhon13NT (98.8%). The complete genome of strain 1-1-2T comprised 1,596,221 bp, with a G+C content of 37.1 mol%. Pairwise comparisons of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain 1-1-2T and its closest phylogenetic neighbours – A. kunkeei DSMZ 12361T, A. nanyangensis HN36-1T and A. apinorum Fhon13NT – revealed ANI values ranging from 80.1% to 93.8% and dDDH values ranging from 22.6% to 52.1%. Strain 1-1-2T can also be distinguished from its closest relatives based on phenotypic and chemotaxonomic characteristics. Accordingly, we propose that strain 1-1-2T represents a novel species within the genus Apilactobacillus, for which the name Apilactobacillus intestinapis sp. nov. is proposed, with 1-1-2T (=BCRC 81468T=NBRC 117233T) as the type strain.

The species Rhizobium panacihumi was isolated from ginseng-cultivated soil in Gochang-gun (South Korea) and only encompassed the type strain DCY116T (=KCTC 62017T=JCM 32251T), which was phylogenetically related to Rhizobium yantingense. Although the species R. yantingense was later reclassified as Endobacterium yantingense, the species R. panacihumi was not transferred to the genus Endobacterium, which currently encompasses the species Endobacterium cereale and E. yantingense. The 16S rRNA phylogenetic analysis showed that strain DCY116T clustered with the type strains of these two species. The phylogenomic analysis of the whole genome of the type strain R. panacihumi KCTC 62017T, which was obtained in this study, confirmed that E. cereale RZME27T and E. yantingense CCTCC AB 2014007T are the closest relatives of R. panacihumi KCTC 62017T. The calculated average nucleotide identity and digital DNA–DNA hybridization values between the genome of this strain and those of E. cereale RZME27T and E. yantingense CCTCC AB 2014007,T together with the results of the phylogenomic analysis, support the reclassification of the species R. panacihumi as Endobacterium panacihumi comb. nov. and the emendation of the genus Endobacterium.

In 2024, bacterial strains KXB24, KXB25 and KXB45 were isolated from sweet corn (Zea mays L.) plants exhibiting foliar chlorosis and streaking, typical symptoms of bacterial infection, in the Everglades Agricultural Area in Florida, USA. A polyphasic taxonomic study was conducted on these strains. Phylogenetic analysis of 16S rRNA gene sequences, whole-genome comparisons and biochemical characterization confirmed that the isolates belong to the Pantoea genus. The Biolog Gen III MicroPlate system identified substrate utilization profiles that were unique to these strains, distinguishing them from closely related Pantoea species. The strain KXB24 showed positive utilization of d-serine, γ-amino-butyric acid, citric acid and other compounds. On nutrient agar, KXB24, colonies are circular, smooth, convex and yellow and do not produce fluorescent pigment on King’s medium B. The DNA G+C content of KXB24 was determined to be 57.0 mol%. Based on phenotypic distinctions, phylogenomics evidence, average nucleotide identity values below 94.26% and digital DNA–DNA hybridization values below 57.9% when compared to type strains of recognized Pantoea species, we propose Pantoea graminicola sp. nov., with KXB24T (=NCPPB 4802T=LMG 33887T) as the type strain. This discovery enriches the current understanding of Pantoea species and calls for further research into the potential role of P. graminicola in sweet corn disease aetiology and its broader agricultural impacts.

A novel carbon monoxide (CO)-oxidizing bacterial strain designated as SB112T was enriched and isolated from Ilex aquifolium leaves from Tocil Wood Nature Reserve in Coventry, UK. The strain was Gram reaction-negative, aerobic, rod-shaped, motile with a polar flagellum and non-spore-forming. Growth of strain SB112T was observed at 10–45 °C, pH 6.0–12.0 and NaCl concentrations of 1–3%. The genomic DNA G+C content was 58.3 mol%, and the major fatty acids (>10%) of strain SB112T were C18 : 1 ω7c, C18 : 1 ω7c 11-methyl and C19 : 0 cyclo ω7c. Major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and a phospholipid. Strain SB112ᵀ contains ubiquinone-10 as the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SB112T formed a separate lineage within the family Phyllobacteriaceae, showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives Aminobacter niigataensis, Aminobacter aminovorans and Mesorhizobium plurifarium, respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family Phyllobacteriaceae. However, its phylogenetic position did not correspond to any known genus within this family. The genome of strain SB112T was found to possess the form II coxL gene, which encodes the large subunit of the CO dehydrogenase and potentially enables CO oxidation. The average nucleotide identity and digital DNA–DNA hybridization with members of closely related genera yielded values below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Based on the phenotypic, chemotaxonomic, phylogenetic, genomic and physiological properties, strain SB112T is considered to represent a novel species of a new genus Foliimonas within the family Phyllobacteriaceae for which the name Foliimonas ilicis gen. nov., sp. nov. is proposed. The type of strain is SB112T (=LMG 33802T, =NCAIM B.02691T).

A Gram-stain-negative, aerobic, ovoid or rod-shaped, non-spore-forming, motile with peritrichous flagella bacterium, designated strain N3-1-1-11T, was isolated from the xylem tissues of Eucalyptus grandis × Eucalyptus urophylla in Qinzhou, Guangxi Province, China. Optimal growth occurred at 28 °C, at pH 6.0 and in the presence of 0–1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that N3-1-1-11T was clustered with species of the genus Caballeronia and formed a distinct sublineage, showing the highest similarities to Caballeronia mineralivorans PML1(12)T (98.48%), Caballeronia udeis LMG 27134T (97.99%) and Caballeronia sordidicola LMG 22029T (97.86%). The predominant ubiquinone is Q-8. The major fatty acids are C16 : 0, C17 : 1  ω5c, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and C18 : 1  ω7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophospholipid. The DNA G+C content was 59.33 mol%. The phylogenetic analysis and physiological and biochemical data showed that strain N3-1-1-11T should be classified as representing a novel species in the genus Caballeronia, for which the name Caballeronia eucalypticola sp. nov. is proposed. The type strain of C. eucalypticola is N3-1-1-11T (=CFCC 15711T=CGMCC 1.65219T=KCTC 8740T).

Three mercury-resistant isolates of a novel Pseudomonas species were obtained from the leaves of coltsfoot (Tussilago farfara L.) growing in mercury-contaminated soil in Southern Poland. Using the 16S rRNA gene sequence, they were identified as likely Pseudomonas arcuscaelestis isolates. Whole-genome analyses based on phylogenomic analyses and overall genome relatedness indices showed that they are three nearly identical isolates of a novel species, with Pseudomonas alkylphenolica KL28T as the closest type species by overall genome relatedness indices [86.64% average nucleotide identity (ANI), 34.2% digital DNA–DNA hybridization (dDDH)] and with P. arcuscaelestis P66T (83.85% ANI, 28.5% dDDH) and Pseudomonas auratipiscis 119PT (83.66% average nucleotide identity, 28.4% dDDH) as the two closest by maximum likelihood phylogenomic analysis. Moreover, five genomes publicly available in the databases were found. One of the three isolates, Hg5Tf, was further characterized as Gram-negative, motile, facultatively aerobic rods, which can be distinguished from closely related species by the (delayed) positive urease reaction in the API20NE test and by weak growth on pectin, d-lactic acid methyl ester and acetoacetic acid in the BIOLOG Gen III test. Matrix-assisted laser-desorption/ionization time-of-flight profile of Hg5TfT is also distinct from those of closely related species. A novel species of genus Pseudomonas is proposed with the name Pseudomonas tussilaginis sp. nov. and Hg5TfT (=CCM 9461T=PCM 3563T) as its type strain.

A novel ascomycetous yeast species of the genus Zygosaccharomyces is proposed, based on isolates obtained in Japan, Portugal and the USA, and on a combination of conventional DNA barcode sequence analyses and whole-genome phylogenies. The new species is described as Zygosaccharomyces progenitor sp. nov. (PYCC 7198T) and was found in association with bees (Apis mellifera and Bombus spp.) and their honey, besides being found in plants and soil. The novel species belongs to a Zygosaccharomyces subclade that also harbours Zygosaccharomyces rouxii. Although the two species can be differentiated at the sequence level, they cannot be distinguished at the phenotypic level. As is typical of the genus, Z. progenitor sp. nov. produces spherical ascospores after cell conjugation.

Three yeast strains closely related to the genus Vanderwaltozyma were isolated from rotting wood (Zelkova serrata) and soil in Japan. Based on sequence analyses of the internal transcribed spacer (ITS1–5.8S–ITS2) region, the D1/D2 domain of the LSU rRNA gene and the mitochondrial COX II gene, together with physiological characterization, these isolates were determined to represent a novel species. The ITS and D1/D2 sequences of the three strains were nearly identical, differing only by a single nucleotide, and their physiological profiles were indistinguishable, supporting their conspecificity. Notably, the strains actively fermented d-glucose and d-fructose. They exhibited tolerance to high osmotic stress, being capable of growth in media containing either 10% sodium chloride with 5% glucose or up to 50% (w/v) glucose. Furthermore, under V8 agar culture conditions, they consistently produced four ascospores per ascus. Phylogenetic analyses based on ITS and LSU D1/D2 sequences clearly placed these strains within the genus Vanderwaltozyma but distinct from other known species. In addition, comparison of COX II gene sequences further supported their separation from related species. Based on these phylogenetic and phenotypic characteristics, we propose Vanderwaltozyma osmotolerans sp. nov. to accommodate these isolates. The holotype of V. osmotolerans sp. nov. is designated as NBRC 117259T.