International journal of systematic and evolutionary microbiology最新文献

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.

Bacterial strains, designated DD3^T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_18 : 0 and C_17 : 0 cyclo. Phylogenetic analyses based on gyrB gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus Afipia; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA-DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95-96 and 70%, respectively), with the highest values observed for Afipia broomeae ATCC 49717^T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3^T/DDX28 constitute a novel Afipia species, for which we propose the name Afipia dichlorophenoxyacetatis sp. nov., with DD3^T (MAFF 311804^T=ICMP 25015^T) as the type strain.

Phytopathogenic bacteria (MAFF 311311^T and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_16 : 0 and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus Acidovorax. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA-DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Acidovorax oryzae ATCC 19882^T (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311^T and MAFF 311313 constitute a novel species within the genus Acidovorax, for which we propose the name Acidovorax sacchari sp. nov., with MAFF 311311^T (=ICMP 25276^T) designated as the type strain.

In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108^T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864^T (JF-1^T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108^T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108^T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108^T (=JCM 39522^T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.