International journal of systematic and evolutionary microbiology最新文献

A Gram-stain-positive, aerobic and non-motile actinobacterium, designated strain MR15.9^T, was isolated from sediment collected from a mangrove ecosystem in Semarang city, Indonesia. Strain MR15.9^T grew at 4-37 °C (optimum 30 °C), pH 6.0-11.0 (optimum 7.0-8.0), with 0-10% (w/v) NaCl (optimum 0-3%). The genome of strain MR15.9^T was 3.67 Mbp with 71.7 mol% G+C content. Phylogenetic analysis based on 16S rRNA gene sequence and genome sequence directed that strain MR15.9^T formed a well-supported clade with Tersicoccus solisilvae CGMCC 1.15480^T and Tersicoccus phoenicis 1P05MA^T and shared the highest similarity to T. solisilvae CGMCC 1.15480^T (98.9% sequence similarity) and T. phoenicis 1P05MA^T (98.6% sequence similarity). However, the comparative genome analysis between strain MR15.9^T and T. solisilvae CGMCC 1.15480^T gave average nt identity value of 85.2% and digital DNA-DNA hybridization value of 29.0%, which were below the statistical threshold for the delineation of the species. Chemotaxonomic data showed that the major fatty acids were anteiso-C_15:0, anteiso-C_17:0 and iso-C_16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. MK-8(H₂) and MK-9(H₂) were noted as the predominant respiratory quinones in this strain. The results of polyphasic characterization indicated that strain MR15.9^T represents a novel species of the genus Tersicoccus. The name Tersicoccus mangrovi sp. nov. is proposed, with the type strain MR15.9^T (=MCCC 1K08875^T=KCTC 59105^T).

A Gram-stain-negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-64^T, was isolated from the rhizosphere of rice. The colonies were observed to be creamy white-coloured, smooth, spherical and 0.5-1.1 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-64^T was able to grow at 10-40 °C, at pH 5.0-9.5 and in the presence of 0-2.0% NaCl (w/v). The strain was positive for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Vogesella and is closely related to Vogesella oryzae L3B39^T (98.6% sequence similarity) and Vogesella facilis TTM-24^T (98.2%). The novel strain MAHUQ-64^T has a draft genome size of 3 827 146 bp (22 contigs), annotated with 3612 protein-coding genes, 74 tRNA and 4 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-64^T and its closest member V. oryzae L3B39^T were 86.5 and 33.4%, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAHUQ-64^T. The genomic DNA G+C content was determined to be 63.4 mol%. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as summed feature 3 (comprising C_{16  :  1} ω7c and/or C_{16  :  1} ω6c) and C_{16  :  0}. Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strain MAHUQ-64^T represents a novel species within the genus Vogesella, for which the name Vogesella oryzagri sp. nov. is proposed, with MAHUQ-64^T (=KACC 22245^T=CGMCC 1.19000^T) as the type strain.

A novel yellow-coloured bacterial strain MA10^T was isolated from mangrove sediment and subjected to polyphasic taxonomic identification. Strain MA10^T was Gram-negative, rod-shaped, catalase-positive and oxidase-positive. Carotenoid pigment was present, and flexirubin-type pigment was absent. The 16S rRNA gene of strain MA10^T had the highest sequence similarity with Tamlana crocina HST1-43^T of 94.5%. The genome size was 3.77 Mbp with a genomic G+C content of 36.3%. The phylogenetic analysis of the 16S rRNA gene sequence and whole-genome sequence showed that strain MA10^T belonged to the genus Tamlana of the family Flavobacteriaceae and tightly clustered with T. crocina HST1-43^T. The digital DNA-DNA hybridization value and average nucleotide identity value between strain MA10^T and T. crocina HST1-43^T were 20.4 and 76.7%, respectively. The major menaquinone was MK-6. The major fatty acids (>10 %) were iso-C_15:0 (41.6%) and iso-C_15:1 G (16.8%). The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. Based on the present polyphasic taxonomic study, strain MA10^T was considered to represent a novel species of the genus Tamlana, for which the name Tamlana flava sp. nov. was proposed. The type strain was MA10^T (=MCCC 1K09289^T=KCTC 102321^T). Additionally, the phylogeny of the 16S rRNA gene and whole-genome sequences found that the hitherto described nine species of the genus Tamlana and Algibacter onchidii presented polyphyletic clades, which could be divided into five different genera. The average amino acid identity value of 80% was chosen as the boundary of the five genera. Thus, except for the genus Tamlana, four novel genera named Allotamlana gen. nov., Cognatitamlana gen. nov., Neotamlana gen. nov. and Pseudotamlana gen. nov. were proposed. This study provided valuable taxonomic analysis of the genus Tamlana.

The genus Actinomadura comprises Gram-positive bacteria found in diverse natural environments and is classified in the family Thermomonosporaceae within the order Streptosporangiales. Some species exhibit considerable phylogenetic and taxonomic overlaps, prompting a comprehensive investigation that integrates phylogenetic, phylogenomic and comparative genomic analyses to elucidate the taxonomic status of two Actinomadura species. Actinomadura livida JCM 3387ᵀ and Actinomadura catellatispora DSM 44772^T shared 16S rRNA gene sequence similarity of 99.9% and digital DNA-DNA hybridization values of 99.8%. Moreover, the average nucleotide identity value for the two species was 99.8%, indicating minimal genomic variation between the two strains. Also, the distribution of carbohydrate-active enzymes and biosynthetic gene clusters predicted to code for secondary metabolites between the two species were almost identical. Data of overall genomic similarity support that Actinomadura catellatispora Lu et al. 2003 be a later heterotypic synonym of Actinomadura livida Lavrova and Preobrazhenskaya 1975 (Approved Lists 1980).

In this article, it is proposed that the Nichols strain of Treponema pallidum be established as the type strain. T. pallidum was first identified as the causative agent of syphilis in 1905, and the Nichols strain was isolated in 1912 by inoculation of a rabbit with cerebrospinal fluid from a patient with neurosyphilis. The Nichols strain has been maintained by serial passage in rabbits for over a century, and historically most studies of T. pallidum have been conducted using this strain. In recent years, a procedure for continuous in vitro culture of T. pallidum in a tissue culture system has been developed, making propagation of this spirochaete easier and hence facilitating research. The Nichols strain has >99% DNA homology with a group of organisms that cause syphilis, bejel/endemic syphilis and yaws in humans, a yaws-like disease in primates and spirochaetosis in rabbits and hares. This group is highly similar in terms of their gene and G+C content, genome synteny, cell morphology, natural dependence on mammalian hosts and ability to cause long-term infections; variation occurs in host range, modes of transmission, aptitude for dissemination, manifestations, congenital infection and geographical distribution. Availability of a type strain will aid in the formal acceptance of T. pallidum subspecies first described in 1984 and supported by recent whole-genome analyses of numerous strains from the T. pallidum-related group.

Three novel strains, designated LB3P45^T, LS2P90^T and ZS1P70^T, were isolated from glaciers located on the Tibetan Plateau, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and yellow or orange coloured. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they belong to the genus Flavobacterium. The 16S rRNA gene sequence similarity among the three strains ranged from 97.4 to 98.6%. Strain LB3P45^T showed 98.9% and 98.7% similarity to Flavobacterium urumqiense CGMCC 1.9230^T and Flavobacterium xinjiangense JCM 11314^T, respectively. Strain LS2P90^T displayed 99.0% and 98.7% similarity to F. xinjiangense JCM 11314^T and F. urumqiense CGMCC 1.9230^T. Strain ZS1P70^T had the highest sequence similarity with F. xinjiangense JCM 11314^T (98.0%) and F. urumqiense CGMCC 1.9230^T (97.8%). The average nucleotide identity and digital DNA-DNA hybridization values between these strains and their closest relatives were lower than 93.0% and 47.9%, respectively. All three strains contained summed feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c) as the major fatty acids. Based on phenotypic characteristics, phylogenetic analysis and genotypic data, the three novel species are proposed: Flavobacterium fructosi sp. nov. (LB3P45^T=CGMCC 1.11439^T=NBRC 114819^T), Flavobacterium xylosi sp. nov. (LS2P90^T=CGMCC 1.11685^T=NBRC 114823^T) and Flavobacterium zhouii sp. nov. (ZS1P70^T=CGMCC 1.24124^T=NBRC 114829^T).

Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name Proteus Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name Proteus Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name Proteus would be undesirable. It is also concluded that Proteus Müller 1786 is an objectively invalid name under the International Code of Zoological Nomenclature. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of Proteus Hauser 1885 (Approved Lists 1980) over Proteus Müller 1786. This action is taken here and makes the prokaryotic name Proteus legitimate.

Two motile bacterial strains, designated as cfHf56-1^T and SW 252, were isolated from the coelomic fluid of Holothuria forskali and from the surrounding seawater at the animal sampling site, respectively. The sea cucumber was collected in the Glénan archipelago (Brittany, France). Strains cfHf56-1^T and SW 252 were Gram-stain-negative, non-spore-forming and rod-shaped bacteria. Colonies made on marine agar plates were brown in color. The pH and temperature ranges for growth were 7-8 and 18-30 °C, respectively, in marine broth. The major fatty acids were 16 : 1 cis9 and 16 : 0. Phylogenetic analyses evidenced that both strains belong to a novel species in the genus Pseudoalteromonas. The strains were closely related to the type strains of Pseudoalteromonas caenipelagi, Pseudoalteromonas byunsanensis and Pseudoalteromonas amylolytica, with 75-78 % ANI and 19-21 % dDDH values. In this context, cfHf56-1^T (= CIP 111854^T = CECT 30642^T) is considered as the type strain of the novel species for which the name Pseudoalteromonas holothuriae sp. nov. is proposed. The genome of the type strain is characterized by a size of 5.1 Mbp and a G+C content of 40.5%.

Two novel Gram-stain-negative, aerobic, heterotrophic, non-motile bacterial strains, designated as AS3R-12^T and PS1R-30^T, were isolated from freshwater in South Korea. To determine their taxonomic positions, the strains were thoroughly characterized. Genomic analyses, based on 16S rRNA gene and draft genome sequence data, revealed that the two novel isolates, AS3R-12^T and PS1R-30^T, belonged to the genus Novosphingobium. AS3R-12^T showed the highest 16S rRNA gene similarity (97.7%) with Novosphingobium flavum UCT-28^T. In addition, PS1R-30^T showed 97.9% 16S rRNA gene similarity with Novosphingobium lentum NBRC 107847^T. The draft genome of strains AS3R-12^T and PS1R-30^T consisted of 4 149 275 and 4 969 838 bps, with DNA G+C content of 63.1 and 66.1 mol%, respectively. The average nucleotide identity between two strains and other related species was below 76.2%, and the digital DNA-DNA hybridization values with closely related species were below 20.8%, both lower than the species delineation threshold. Strains AS3R-12^T and PS1R-30^T contained the ubiquinone Q-10 as the major quinone and displayed a polyamine pattern with spermidine as the predominant polyamine. Additionally, their major fatty acids were characterized by C_16:1  ω7c/C_16:1  ω6c (summed feature 3) and C_18:1  ω7c/C_18:1  ω6c (summed feature 8). The major polar lipids of AS3R-12^T and PS1R-30^T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), sphingoglycolipid (SGL) and phosphatidylcholine (PC). Moreover, physiological and biochemical results allowed the phenotypic and genotypic differentiation of strains AS3R-12^T and PS1R-30^T from their closest and other species of the genus Novosphingobium with validly published names. Therefore, AS3R-12^T and PS1R-30^T represented novel species of the genus Novosphingobium, for which the names Novosphingobium aquae sp. nov. (type strain AS3R-12^T=KACC 23096^T=LMG 32950^T) and Novosphingobium anseongense sp. nov. (type strain PS1R-30^T=KACC 23097^T=LMG 32951^T) are proposed.

Ciliates of the class Nassophorea Small & Lynn, 1981, inhabit a wide range of aquatic environments and serve as a trophic link in microbial food webs. However, their diversity remains underestimated. In the present study, the morphology and molecular phylogeny of Rhinakis faurei Deroux, 1994, an insufficiently known nassulid ciliate, were investigated using an integrative taxonomic approach. The studied population was collected from a freshwater pond in Qingdao, China. Details of the live morphology and ciliature of R. faurei are documented for the first time, and an improved species diagnosis is provided. Phylogenetic analyses of the small subunit ribosomal RNA gene sequence revealed that R. faurei clusters within the family Nassulidae de Fromentel, 1874. However, evolutionary interrelationships within the Nassulidae remain obscure owing to under-sampling, the lack of sequence data for most nominal species, and low nodal support or unstable gene tree topologies.