Bats, of the order Chiroptera, comprise over 1,400 species and account for over 21% of all currently described mammalian species. However, despite this huge group of mammals, a remarkably small number of bacterial species have been described from this group. In a continuing study of non-human mammals, dozens of strains were isolated from anaerobic guano-pile enrichments collected in a bat cave near Protem, MO, USA. Of these, two novel taxa were identified and designated BS-2T and BS-20T; both were rod-shaped, Gram-stain-positive bacteria. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis placed BS-2T within the genus Lacrimispora, and BS-20T was located within the family Jonesiaceae, but with no particular affiliation to any genus. Overall genomic-based relatedness indices indicated that strains BS-2T and BS-20T shared average nucleotide identity and digital DNA-DNA hybridization values <95.0% and <70.0% with their nearest neighbouring taxa, which are the currently accepted thresholds for species-level delineation. Further, for strain BS-20T, genus-specific delineation indices demonstrated a shared average amino acid identity, and percentages of conserved proteins were <68.0% and <42.0%, respectively, between BS-20T and other Jonesiaceae taxa, below commonly accepted genus-level delineation thresholds. The predominant cellular fatty acid of isolate BS-2T was C16:0, whereas BS-20T contained C15:0 anteiso and C14:0 as the predominant cellular fatty acids. The G+C content of BS-2T and BS-20T was 44.1 and 56.5 mol%, respectively. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, strains BS-2T and BS-20T represent novel isolates within the genus Lacrimispora and family Jonesiaceae, for which the names Lacrimispora cavernae sp. nov. and Aleya cavernae gen. nov., sp. nov. are proposed. Strains BS-2T (=NRRL B 65694T=CCUG 77247T=CCM 9410T) and BS-20T (=NRRL B-65699T=CCUG 77269T) are proposed as the type species of these novel taxa.
Two Gram-stain-negative, aerobic, oxidase-negative, non-motile, ellipsoid to short rod-shaped bacteria (~1.2-2.0 µm in length and 0.7-0.8 µm in width) were isolated from soil near a wastewater treatment plant in Hangzhou, Zhejiang Province, China, designated TB0136T and TB0139T. Both strains are able to grow chemolithoautotrophically using hydrogen as an electron donor and perform nitrogen fixation in the absence of ammonium or any organic nitrogen source. Strains TB0136T and TB0139T were observed to grow at temperatures of 15-45 °C (both optimal at 33 °C; TB0139T additionally showed trace growth at 50 °C), at pH of 6.0-10.0 (TB0136T optimal at 7.5-8.0, TB0139T optimal at 8.0-8.5) and in the presence of 0-6.0% (w/v) NaCl (optimal at 1.0%). Chemotaxonomic analyses indicated that the main respiratory quinone in both strains is ubiquinone-10. The DNA G+C contents of strains TB0136T and TB0139T were 63.3 and 61.5 mol%, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence and the whole genome indicated that strains TB0136T and TB0139T formed a unique lineage in the evolutionary branches of the family Xanthobacteraceae. According to the characteristics of polyphasic taxonomy, strains TB0136T and TB0139T are proposed to represent two novel species of a new genus, for which the name Haloleucobacter gen. nov. is proposed. The proposed species names are Haloleucobacter ellipsoideus and Haloleucobacter albus. The type strains are TB0136T (=MCCC 1K09187T=JCM 37006T) and TB0139T (= MCCC1K09185T=JCM 37007T), respectively.
Four strains of coliform bacteria were isolated from drinking water (strains A2-C1_F and A2-C2_NF) and gastropod samples (strains W03-F01T and S04-F03). 16S rRNA gene sequence analysis showed the highest similarities to members of the genus Buttiauxella (>98%), indicating that all strains are members of this genus. Phylogenomic analyses revealed that strains W03-F01T, S04-F03 and A2-C1_F can be assigned to a putative new Buttiauxella species, while strain A2-C2_NF is a member of the species Buttiauxella ferragutiae. The strains W03-F01T, S04-F03 and A2-C1_F show fluorescence in the Colilert system, indicating unusual β-d-glucuronidase activity, typically considered indicative for Escherichia coli (and thus faecal contamination) in water quality analysis. The draft genome of strain W03-F01T has a size of 4.79 Mb and a G+C content of 50.0 mol%. With average nucleotide identity and digital DNA-DNA hybridization values of 96.2 and 68.8%, respectively, strain W03-F01T was most closely related to Buttiauxella massiliensis DSM 110695T. Additional extensive physiological, phenotypic and chemotaxonomic characterization of the strains and all reference strains confirmed the proposal of a novel species. Therefore, the strains W03-F01T, S04-F03 and A2-C1_F represent a novel species for which the name Buttiauxella cochleicola sp. nov. is proposed. The type strain is W03-F01T (=DSM 113920T=CIP 112567T).
In a previous study, an isolate identified as Akanthomyces sensu lato, obtained from the citrus blackfly Aleurocanthus woglumi in Brazil, was shown to be pathogenic towards its host. Phylogenetic evidence indicated that this isolate belongs to a new taxon. This study aimed to describe this new taxon based on both morphological and molecular phylogenetic markers, to assess its potential for the biological control of the conehead termite (Nasutitermes corniger) and the citrus orthezia (Praelongorthezia praelonga) and to evaluate substrates for the mass production of this fungus. Phylogenetic analysis based on TEF1, RPB1, RPB2 and ITS partial sequences demonstrated that this new species is related to Lecanicillium aranearum, Lecanicillium araneicola, Lecanicillium rasoulzarei and Lecanicillium spenceae. However, these species form a clade that corresponds to neither Akanthomyces sensu stricto nor Lecanicillium sensu stricto. Therefore, a new genus Allolecanicillium is proposed here to accommodate Allolecanicillium elzae sp. nov., Allolecanicillium aranearum comb. nov., Allolecanicillium araneicola comb. nov., Allolecanicillium rasoulzarei comb. nov. and Allolecanicillium spenceae comb. nov. These species produce dense white to cream mycelia and simple or branched conidiophores bearing cylindrical to fusoid conidia. The sexual morph is known only for the species A. aranearum. Sporulation of A. elzae on vegetable substrates ranged from 1.46×108 conidia/g of substrate (white rice) to 6.42×108 conidia/g of substrate (sugarcane bagasse). Germination rates did not differ significantly among substrates. Despite being pathogenic to P. praelonga and N. corniger, this fungus showed relatively low virulence against these insects under the conditions tested. This research expands our knowledge of the diversity of entomopathogenic fungi, their host spectrum and alternatives for their production, aiming to foster the recognition of these organisms as sustainable biological resources.
The ascomycete genus Taphrina comprises dimorphic plant-parasitic pathogens, several species of which cause plum pockets. Plum pocket pathogens on Japanese plum (Prunus salicina) were collected from seven localities in Korea, including Gimcheon (KCTC 37381T/KACC 411123), Gumi, Okcheon (KCTC 37382/KACC 411126), Boeun, Jeonju, Wanju (KACC 410969) and Naju (KCTC 37383/KACC 411129). Based on a polyphasic approach combining morphological and physiological characterization with a molecular phylogenetic analysis involving the internal transcribed spacer (ITS) region, the D1/D2 domain of the 26S rRNA gene and the mitochondrial small subunit ribosomal RNA (rns) gene, these isolates were confirmed to represent a novel Taphrina species. Phylogenetically, the novel species was closely related to a clade comprising Taphrina pruni and Taphrina mume, which cause plum pocket disease and apricot leaf curl, respectively. Compared with the type strain of T. pruni (HA 1306ᵀ), the new Korean isolates exhibited low sequence similarity, with 95.79%, 98.95% and 98.77% identities in the ITS, D1/D2 domain and rns regions, respectively. Isolates infecting P. salicina formed an independent clade distinct from all known Taphrina species. The isolates also differed from T. pruni in ascospore size, budding rate within asci and cultural characteristics. Physiologically, the isolates differed from T. pruni HA 1306ᵀ in 7 of 41 carbon assimilation tests, 4 of 10 nitrogen assimilation tests, and growth at 25 ℃. To date, plum pocket pathogens on P. salicina have been attributed to T. pruni, Taphrina communis and Taphrina deformans; however, the present study shows that they represent a novel species. We propose the name Taphrina neopruni sp. nov. (MycoBank number MB 862651) and designate KCTC 37381T (ex-type strain KACC 411123) as the holotype.
Five Gram-negative strains, designated BI01T, BI02, BI1211, BI4D and BI67 isolated from the gut of the Antarctic endemic insect Belgica antarctica, were characterized by a polyphasic approach. Comparative 16S rRNA gene sequences indicated that the bacterial strains belonged to the genus Yersinia. A cgMLST-based phylogeny based on 500 concatenated core genes strongly supported a clade encompassing the 5 strains that was distinct from the currently recognized 27 species of the genus Yersinia. Average nucleotide identity (ANI) among the five strains consistently exceeded 99%, but comparisons to their closest relative, Yersinia intermedia, yielded an ANI of 93% and a digital DNA-DNA hybridization value of 51.74. Metabolic profiling further differentiated the five strains from other closely related species within the genus Yersinia, notably with respect to l-fucose and potassium 2-ketogluconate fermentation, acetoin production and an absence of pyrazinamidase activity. Interestingly, three of the five strains exhibited resistance to β-lactams (amoxicillin and amoxicillin/clavulanate) and first- and second-generation cephalosporins (cefalexin and cefoxitin) associated with the presence of the ampC gene, encoding a class C beta-lactamase, in their genome. None of the five isolates harbour the classic virulence determinants of enteropathogenic Yersinia. The DNA G+C content of the five strains is 47.8 mol%. Based on these results, they represent a novel species of the genus Yersinia, for which the name Yersinia antarctica sp. nov. is proposed. Notably, this represents the first Yersinia species reported from Antarctic terrestrial invertebrates. The type strain is BI01T (=CIP 112622T=DSM 121309T). The distribution of this species is not limited to Antarctica, as few publicly available genomes indicate its presence in continental Russia and the Russian Arctic, with isolates recovered from rodents, polar bears and birds.
Two Gram-stain-positive, catalase-positive, oxidase-negative, non-spore-forming, aerotolerant anaerobic and non-motile short rod-shaped bacterial strains, designated V947T and V970, were isolated from nasal swab samples of coal miners. Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome sequences revealed that strains V947T and V970 represent a distinct lineage within the genus Cutibacterium, most closely related to Cutibacterium avidum ATCC 25577T (16S rRNA gene sequence similarity of 97.09%). Whole-genome comparative analyses showed that the average nucleotide identity values between the two strains and all validly published species of the genus Cutibacterium with correct nomenclature ranged from 76.55 to 90.26%, while the digital DNA-DNA hybridization values ranged from 21.80 to 40.40%, both of which are well below the accepted thresholds for species delineation. Pangenome analysis identified 711 species-specific gene clusters present in strains V947T and V970 but absent from all reference type strains of the genus, which were predominantly involved in carbohydrate transport and metabolism, inorganic ion transport and signal transduction mechanisms, suggesting distinct metabolic capabilities and potential for environmental adaptation. These genomic features not only support the delineation of a novel species but also expand the known genomic and functional diversity within the genus Cutibacterium. The predominant cellular fatty acids were iso-C15:0 and anteiso-C15:0. The major polar lipids of strain V947T were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine, and the predominant menaquinones were MK-8(H4) and MK-9(H6). On the basis of phylogenetic, genomic, chemotaxonomic and phenotypic characteristics, strains V947T and V970 represent a novel species of the genus Cutibacterium, for which the name Cutibacterium nasicola sp. nov. is proposed. The type strain is V947T (=CGMCC 1.5844T=KCTC 59608T).
Strain 17KM0847T, isolated from the nasal discharge of a dead captive Cape ground squirrel (Xerus inauris), is a Gram-positive, oxidase-negative, catalase-positive and coagulase-negative coccoid bacterium. It grows under both aerobic and anaerobic conditions at 37 °C and tolerates up to 17.5% NaCl, and its colonies are smooth, convex and circular and exhibit complete staphylococcal α-haemolysis on sheep and horse blood agar. Phylogenomic analysis based on DNA alignment and amino-acid alignment obtained from the translated whole-genome sequence, along with comparisons of 16S rRNA and housekeeping genes (hsp60, dnaJ, rpoB, sodA, gap and tuf), placed strain 17KM0847T within the genus Staphylococcus, most closely related to species of Staphylococcus muscae, Staphylococcus microti, Staphylococcus rostri and Staphylococcus americanisciuri. The strain exhibited digital DNA-DNA hybridization (dDDH) values ≤22% and average nucleotide identity (ANI) values <78% to these closest relatives, well below the species-level delineation thresholds (70% dDDH; 95% ANI). Chemotaxonomic analysis identified diphosphatidylglycerol, phosphatidylglycerol and an aminophospholipid as the major polar lipids. The cellular fatty acid profile was dominated by C20 : 0, iso-C15 : 0, C16 : 0 and C18 : 0. The peptidoglycan contained type A3αl-Lys-Gly4-l-Ser-Gly. Based on chemotaxonomic and genomic characteristics, strain 17KM0847T (=DSM 120281T; =CCOS 2136T; =CCM 9521T) represents a novel species of the genus Staphylococcus, for which the name Staphylococcus xeri sp. nov. is proposed.
The Senate of The University of Queensland, on the recommendation of the Executive Board of the International Committee on Systematics of Prokaryotes, is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the quadrennium 2020-2024 to Professor Jon Jongsik Chun in recognition of his contributions made to the field of bacterial systematics. The award, established in 1986 by Professor V.B.D. Skerman of the Department of Microbiology at the University of Queensland, honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel.
Eight bacterial strains assigned to the genus Arthrobacter by preliminary 16S rRNA gene screening were isolated from supraglacial samples collected from four glaciers in China. Genome-based analyses provided the primary evidence for species delineation. Pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons among the eight strains and between the glacier-derived strains and their closest type-strain relatives supported their assignment to six novel species, with strains HZ1T and HLT1-21 (ANI 99.1%, dDDH 92.2%) and strains MDB2-24T and MDT3-44 (ANI 98.5%, dDDH 87.9%) each representing a single genomic species. Consistently, a maximum-likelihood phylogenomic tree inferred from 81 concatenated bacterial core genes resolved 6 well-supported independent species-level lineages within the Arthrobacter agilis group. The predominant cellular fatty acid of the representative strains was anteiso-C15 : 0 (34.5-66.1%). In addition, genome-relatedness indices indicated that Arthrobacter vasquezii Valenzuela-Ibaceta et al. 2023 is conspecific with Arthrobacter parietis Heyrman et al. 2005 (ANI 98.8%, dDDH 90.1%) and should, therefore, be treated as a later heterotypic synonym of A. parietis Heyrman et al. 2005 under the principle of priority. Based primarily on phylogenomics and genome relatedness, supplemented by phenotypic and chemotaxonomic characterization, the eight strains represent six novel species of the genus Arthrobacter, for which the following names are proposed: Arthrobacter glycogeni sp. nov. (HZ1T=CGMCC 1.9261T=JCM 38152T), Arthrobacter arabinosi sp. nov. (TMS1-12-1T=CGMCC 1.9392T=NBRC 113087T), Arthrobacter melezitosi sp. nov. (TMN-37T=CGMCC 1.9692T=JCM 38156T), Arthrobacter sorbitolis sp. nov. (MDT1-65T=CGMCC 1.9836T=JCM 38163T), Arthrobacter rhamnosi sp. nov. (MDB2-24T=CGMCC 1.9862T=JCM 38160T) and Arthrobacter pasteuri sp. nov. (MDT2-2T=CGMCC 1.9874T=JCM 38164T).
The taxonomic boundaries of Pseudomonas moraviensis remain unclear despite the increasing availability of genomic data. In this study, we performed a comprehensive polyphasic taxonomic reassessment of 30 publicly available strains, together with 2 newly isolated wheat rhizosphere strains, S9433 and S9602, which exhibited genomic and phenotypic traits indicative of plant growth-promoting potential. Phylogenetic and phylogenomic analysis consistently revealed that strains currently assigned to P. moraviensis are distributed across several distinct lineages. Overall genomic relatedness indices, including average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH), supported the reclassification of multiple strains into different Pseudomonas species. Twenty-two strains including S9433 and S9602 were confirmed as P. moraviensis, whereas five were reclassified as Pseudomonas atacamensis, two as Pseudomonas parakoreensis and one as Pseudomonas iranensis. Strain #71, formerly designated as the type strain of P. moraviensis subsp. stanleyae, formed a distinct phylogenetic lineage with ANIb and dDDH values below species delineation thresholds and a divergent fatty acid profile, collectively indicating that it represents a novel species. Strain VanB exhibited ambiguous genomic relatedness to Pseudomonas aphyarum, Pseudomonas paraglycinae and Pseudomonas fitomaticsae, with ANIb values approaching but dDDH values well below species delineation thresholds, leaving its taxonomic status unresolved pending further investigation. This study clarifies and resolves the taxonomic status of currently assigned P. moraviensis strains and lays a foundation for the functional characterization and applied utilization of this species complex.
Five crocodilian species were investigated for the presence of Pasteurellaceae. A total of 27 pharyngeal isolates were obtained and characterized by MALDI-TOF MS and preliminary phenotypic tests to enable selection of representative strains for further genotypic characterization. Twelve isolates were selected for sequencing followed by phylogenetic analyses, digital DNA-DNA hybridization (dDDH) and calculation of average nucleotide identity (ANI), in addition to comparative analyses of partial rpoB, 16S rRNA gene sequences and further phenotypic characterization. The phenotypic and genotypic comparisons grouped the strains into three clades (clade 1: n=4; clade 2: n=3; clade 3: n=5). The clade 3 strains had a 16S rRNA gene sequence similarity ranging from 94.8 to 96.5%, a dDDH value of ≤48.7% and an ANI value of ≤92.6% to the closest relative, Testudinibacter aquarius ELNT2xT, and could be distinguished from all current Pasteurellaceae species by a combination of phenotypic traits. Our results indicate that the clade 3 strains should be classified as representatives of a new Testudinibacter species for which we suggest Testudinibacter crocodili sp. nov. The type strain of T. crocodili is Cuba42T (=CCUG 77853T=DSM 118260T) and was isolated in Denmark in 2018 from the pharynx of a captive Cuban crocodile (Crocodylus rhombifer).
This article represents the valid publication of the names of three subspecies of Treponema pallidum . These subspecies were first described by Robert M. Smibert in 1984 and correspond with organisms that cause syphilis (subsp. pallidum ), yaws (subsp. pertenue ) and bejel (subsp. endemicum ) in humans. The subspecies nomenclature has been widely used in the literature since that time but has not been validly published due in part to the availability of only limited genetic information. The designation of these subspecies is now supported by a large number of genomic sequences indicating a clear separation of these three closely related yet genetically distinct groups, as demonstrated in this study by phylogenetic analysis of a representative group of strains from each subspecies and the closely related lagomorph pathogen Treponema paraluiscuniculi . Subspecies-specific regions were also identified by genomic comparisons to provide an additional means of distinguishing the T. pallidum subspecies and T. paraluiscuniculi without complete genomic sequencing. Finally, the Gauthier T (=BEI Resources NR-60826 T =DSM 120346 T ) and Bosnia A T (=BEI Resources NR-60824 T =DSM 120347 T ) strains are herein designated as the type strains of T. pallidum subsp. pertenue and T. pallidum subsp. endemicum , respectively, whereas Nichols T (=BEI Resources NR-59701 T =DSM 117211 T ) and SS14 (=BEI Resources NR-60825=DSM 120345) represent type and reference strains of T. pallidum subsp. pallidum , respectively. Overall, this article corroborates the many prior reports that support the formal establishment of the three T. pallidum subspecies and provides additional guidelines for their distinction.
A Gram-stain-positive, aerobic, non-motile, non-sporulating and rod-shaped actinobacterium, designated strain S7RM1-6T, was isolated from a root of the mangrove plant Acanthus ilicifolius collected from Beihai City in Guangxi Zhuang Autonomous Region, China. The cells of strain S7RM1-6T were catalase-positive and oxidase-negative and grew at temperatures of 15‒40 °C (optimum, 37 °C), at pH 6.0‒9.0 (optimum, pH 7.0-8.0) and in the presence of 0‒5% (wt/v) NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain S7RM1-6T was affiliated with members of the genus Patulibacter and shared the highest 16S rRNA gene sequence similarities with Patulibacter minatonensis DSM 18081T (97.9%) and Patulibacter americanus DSM 16676T (97.9%). The draft genome of strain S7RM1-6T displayed a size of 3.7 Mbp with a DNA G+C content of 75.0 mol%. Phylogenomic analysis based on whole-genome sequences indicated strain S7RM1-6T should be assigned to the genus Patulibacter. The highest average nucleotide identity and digital DNA-DNA hybridization values between strain S7RM1-6T and its closest type strain P. americanus DSM 16676T were 80.9 and 24.7%, respectively. The chemotaxonomic characteristics supported its placement within the genus Patulibacter, with meso-diaminopimelic acid as the diagnostic peptidoglycan diamino acid, demethylmenaquinone 7 as the predominant respiratory quinone and C18:1 ω9c and anteiso-C15:0 as the major fatty acids. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, five unknown glycolipids, two unidentified phospholipids and one unidentified aminolipid. Genomic and phenotypic analyses revealed adaptive traits consistent with an endophytic lifestyle associated with A. ilicifolius, including enhanced osmotic stress tolerance, a reduced secondary metabolome and versatile carbon utilization capacity. These results support the classification of strain S7RM1-6T as a novel species of the genus Patulibacter, for which the name Patulibacter endophyticus sp. nov. is proposed. The type strain is S7RM1-6T (= KCTC 59613T = CPCC 206827T).
A polyphasic taxonomic study was carried out on two bacteria isolated from the roots of aquatic plants, designated as strains T5W1-RT and T9W2T. Both are Gram-negative, rod-shaped, non-motile and aerobic bacteria. Strain T5W1-RT is red-pigmented and produces bacteriochlorophyll, while strain T9W2T is yellow and does not produce bacteriochlorophyll. Nearly complete 16S rRNA gene sequence homology related T5W1-RT to Erythrobacter, with 99.0 and 98.9% similarity to Erythrobacter dokdonensis DSM 17193T and Erythrobacter fulvus KACC 22865T, respectively, and T9W2T to Sphingomonas, with 99.2 and 99.0% similarity to Sphingomonas hankookensis KCTC 22579T and Sphingomonas lacusdianchii KCTC 72813T, respectively. DNA G+C content for T5W1-RT and T9W2T was 63.5 and 65.5 mol%, respectively. Average nucleotide identity and digital DNA-DNA hybridization with the closest phylogenetic neighbours of each isolate showed differences at the species level, further confirmed by differences in several physiological characteristics. The predominant fatty acids for T5W1-RT were C18:1 ω7c, C17:1 ω6c and C16:0, while T9W2T contained C18:1 ω7c, C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C14:0 2-OH. Both strains had ubiquinone 10 as the primary ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid as the dominant polar lipids. Based on the results obtained, these bacteria are new species with T5W1-RT assigned to the genus Erythrobacter with the name Erythrobacter epiphyticus sp. nov., type strain T5W1-RT (=NRRL B-65716T=DSM 118060T), and T9W2T assigned to the genus Sphingomonas with the name Sphingomonas epibiotica sp. nov., type strain T9W2T (=NRRL B-65717T=DSM 118105T).
Two novel bacterial strains, designated as 2405UD66-6T and 2405UD68-3T, were isolated from marine algae collected in the Republic of Korea. Both strains were Gram-stain-negative, strictly aerobic, motile, rod-shaped and oxidase-positive. Optimal growth occurred at 28 °C and pH 7.0, with NaCl concentrations of 3.0-4.0% (w/v) for strain 2405UD66-6T and 2.0-3.0% (w/v) for strain 2405UD68-3T. Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on draft genome sequences revealed that strains 2405UD66-6ᵀ and 2405UD68-3ᵀ belong to the genus Marinomonas. Phylogenomic analysis revealed that strain 2405UD66-6T was most closely related to Marinomonas colpomeniae SM2066T, while strain 2405UD68-3T was most closely related to Marinomonas phaeophyticola 15G1-11T. Average nucleotide identity and digital DNA-DNA hybridization values between strain 2405UD66-6T and its closest relative were 77.4 and 20.6%, respectively, whereas those between strain 2405UD68-3T and its closest relative were 75.8 and 19.7%, respectively. These values are well below the accepted species delineation thresholds, indicating that both strains represent novel species within the genus Marinomonas. The genomic G+C contents for strains 2405UD66-6T and 2405UD68-3T were 42.5 and 40.5 mol%, respectively. The major polar lipids of both strains were phosphatidylglycerol and phosphatidylethanolamine, and the sole respiratory quinone was ubiquinone-8. The predominant fatty acids (>10.0%) in both strains were C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Based on a polyphasic taxonomic approach, the names Marinomonas algae sp. nov. and Marinomonas phycocola sp. nov. are proposed, respectively. The type strain is 2405UD66-6T (KACC 24016T=MCCC 1K09776T) for M. algae and 2405UD68-3T (KACC 24017T=MCCC 1K09819T) for M. phycocola.
Two Gram-staining positive, aerobic, non-motile, endospore-forming and rod-shaped bacteria, designated strains SI92T and SI8, respectively, were isolated from the rhizosphere soil of tobacco collected from south-western China. Strain SI92T shared the highest 16S rRNA gene similarity to Paenibacillus silvestris (97.9%) and Paenibacillus phytorum (97.9%), and strain SI8 showed the highest 16S rRNA gene similarity with P. phytorum (98.0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SI92T and SI8 clustered with the genus Paenibacillus and formed a distinct subclade. Growth of strains SI92T and SI8 occurred at 15-45 °C, pH 6.0-8.0 (optimum pH 7.0) and with 0-1.0% (wt/vol) NaCl on R2A medium. The respiratory quinones of strains SI92T and SI8 were identified as menaquinone-7. The predominant cellular fatty acids (>10.0%) were identified as anteiso-C15 : 0. The profile of polar lipids contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the average nucleotide identity values and the digital DNA-DNA hybridization values with most closely related strains, strains SI92T and SI8 belonged to the same species and represented a novel species of the genus Paenibacillus, for which the name Paenibacillus tabacirhizosphaerae sp. nov. (type strain SI92T=CGMCC 1.19445T=NBRC 115451T) is proposed.
Eleven glacier-derived bacterial strains, represented by the type strains HZ3T, TMT1-37T, TMS2-18T, TMN-17T, TMN-24T, MDT1-20T, MDT3-30T, HLT3-6T and MDT3-24T, were isolated from cryoconite samples collected from glaciers in China. These strains comprised nine genomic species because TMN-24T and TMT1-38, and MDT1-20T and HLT1-8, respectively, represented two conspecific pairs. The 16S rRNA gene sequence identities among the 11 strains ranged from 98.68 to 100% and their closest phylogenetic neighbours were species of the genus Pseudarthrobacter. Phylogenomic analysis based on 81 concatenated core genes placed the 11 strains within the genus Pseudarthrobacter and resolved them into distinct lineages. Pairwise average nucleotide identity values between the novel strains and their closest relatives were 80.10-94.80%, and the corresponding digital DNA-DNA hybridization values were 22.6-59.5%, all below the accepted species delineation thresholds, except for the two conspecific strain pairs TMN-24T/TMT1-38 and MDT1-20T/HLT1-8. The genomic DNA G+C contents of the type strains ranged from 64.6 to 66.9 mol%. Differential phenotypic characteristics further supported their separation from recognized species of the genus. On the basis of the polyphasic taxonomic evidence, nine novel species of the genus Pseudarthrobacter are proposed: Pseudarthrobacter ribosi sp. nov. (type strain HZ3T=CGMCC 1.9263T=NBRC 117320T), Pseudarthrobacter leeuwenhoeki sp. nov. (TMT1-37T=CGMCC 1.9345T=NBRC 117321T), Pseudarthrobacter linnaei sp. nov. (TMS2-18T=CGMCC 1.9408T=NBRC 117322T), Pseudarthrobacter adonitolis sp. nov. (TMN-17T=CGMCC 1.9575T=NBRC 117323T), Pseudarthrobacter kochi sp. nov. (TMN-24T=CGMCC 1.9581T=NBRC 117324T), Pseudarthrobacter woesei sp. nov. (MDT1-20T=CGMCC 1.9798T=NBRC 117325T), Pseudarthrobacter xylosi sp. nov. (MDT3-30T=CGMCC 1.9921T=NBRC 117328T), Pseudarthrobacter lactosi sp. nov. (HLT3-6T=CGMCC 1.10016T=NBRC 117330T) and Pseudarthrobacter arbutini sp. nov. (MDT3-24T=CGMCC 1.9916T=JCM 38166T).
Bee-associated Orbaceae species aid in the metabolism of plant polysaccharides, toxic sugars and urea and stimulate the immune system. In honeybees and other eusocial bees, microbial transmission occurs through hive contact and social interactions, favouring the emergence of host-specific strains. While most solitary bees acquire their microbiota from the environment, large carpenter bees (genus Xylocopa) exhibit facultative or incipient social behaviour that might enable direct transmission. This behaviour might have contributed to host specialization of Xylocopa-associated bacteria, such as the genus Xylocopilactobacillus and novel species belonging to the genus Lactobacillus and the family Bifidobacteriaceae. Evidence of an apparent Xylocopa-specific Orbaceae clade has also been observed. Here, we isolated and characterized AC157XtpT, a novel strain in the family Orbaceae, from the gut of Xylocopa tabaniformis parkinsoniae. The optimal growth occurs anaerobically at 30-35°C, 0-0.5% salinity and pH 6-7. The predominant fatty acids were C18:1 ω6c and/or C18:1 ω7c (45.9%), followed by C16:0 (35.0%) and C14:0 (7.8%), consistent with those reported for members of the family Orbaceae. The cell size of AC157XtpT was ~0.5-1.6 µm in length and 0.4-0.7 µm in width, with coccoid to small rod-shaped morphology under scanning electron microscopy. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) scores between AC157XtpT and other Orbaceae ranged from 69.99 to 72.88% for ANIb, from 0.59 to 0.83 for TETRA values and from 20.1 to 26.7% for dDDH, measures far below species thresholds. Combined with the average amino acid identity (AAI) and percentage of conserved proteins (POCP) at the lower end of the Orbaceae-specific genus boundary range, and the phylogenomic tree placing AC157XtpT in a separate monophyletic clade sister to Orbus and Frischella, these data support the classification of AC157XtpT as a representative of a novel genus within the family Orbaceae. In conclusion, AC157XtpT (=NCIMB 15593T=ATCC TSD-486T) represents the type strain of Neffella xylocopae gen. nov., sp. nov. The GenBank accession numbers are CP133583 (genome) and PQ456091 (16S rRNA gene).
