International journal of systematic and evolutionary microbiology最新文献

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.

Three strains, designated as J27, J71^T and J72, belonging to the genus Antrihabitans, were isolated from stable foams formed in activated sludge wastewater treatment plants (WWTPs) in New South Wales, Australia. Phenotypic and genomic analyses revealed that these strains belong to the Nocardiaceae family and are closely related to Antrihabitans stalagmiti. However, distinct genomic and physiological characteristics, including overall genomic relatedness indices, phylogenomic analysis, genomic metabolic profiles and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry), confirmed their status as a new species.Ecologically, these strains showed a wide metabolic versatility, like enhanced membrane transport systems for amino acids, metals and phosphate, as well as the ability to synthesize mycolic acids, contributing to their hydrophobic nature and involvement in foam stabilization. Their adaptations likely provide a competitive advantage in WWTPs, where they persist in nutrient-rich, metal-laden and foam-stabilizing environments. The species did not present the typical rod-coccus cycle, described previously as a defining characteristic of the Antrihabitans genus. Based on their unique genomic, phenotypic and ecological features, we propose the name Antrihabitans spumae sp. nov., with strain J71^T (JCM 34493^T, NCIMB 15450^T) designated as the type strain. Additional strains include J27 (JCM 33914, NCIMB 15449) and J72 (NCIMB 15448).

Three novel coccoid-shaped strains, designated 21WXBC0057M1^T, 21WXBC0044M1^T and BJSWXB5TM5^T, were isolated from human breast milk in Wuxi, Jiangsu Province, China. These strains were facultative anaerobes, catalase-negative and Gram-positive. Through a comprehensive analysis of rRNA genes, protein-coding housekeeping genes and genomic phylogeny, we identified these strains as belonging to the genus Streptococcus. Specifically, strain 21WXBC0057M1^T was phylogenetically most closely related to Streptococcus infantis, strain 21WXBC0044M1^T was most closely related to Streptococcus oralis and strain BJSWXB5TM5^T displayed similarities to Streptococcus australis, Streptococcus peroris and S. infantis. The pairwise average nucleotide identity and digital DNA-DNA hybridization values for these three strains were below 95 and 70%, respectively, indicating that they occupied evolutionary branches distinct from all previously validly published Streptococcus species. Distinctive phenotypic characteristics discriminated these novel species from the type strains of their most closely related species. The major cellular fatty acids in the three strains were C_16 : 0 and C_18 : 0. Genome annotation and a thorough examination of carbohydrate-active enzyme distribution highlighted the observation that all strains possessed extensive capabilities for carbohydrate metabolism, particularly human milk oligosaccharides utilization. Thus, based on these findings, we proposed the classification of the strains as representing three novel species within the genus Streptococcus: Streptococcus wuxiensis sp. nov. (type strain 21WXBC0057M1^T=GDMCC 1.4126^T=KCTC 25760^T), Streptococcus jiangnanensis sp. nov. (type strain 21WXBC0044M1^T= GDMCC 1.4127^T=KCTC 25762^T) and Streptococcus fermentans sp. nov. (type strain BJSWXB5TM5^T=GDMCC 1.4130^T=KCTC 25759^T).

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-01^T, was isolated from the sediment sample of the piston core collected at station 3 at Good Weather Ridge area offshore southwestern Taiwan from ORI-902A cruise in 2009. Cells of strain CWC-01^T are rod-shaped, measuring 0.4-0.5 µm in width and 1.0-2.0 µm in length. Strain CWC-01^T utilizes formate and H₂/CO₂ to produce methane, but not secondary alcohol, methanol, ethanol, methylamines or acetate as catabolic substrates. The optimal growth conditions are 37 °C, 0.043 M NaCl and pH 6.3. Growth effectors tests indicate tryptone, but not acetate and yeast extract, could stimulate the growth of strain CWC-01. Phylogenetic analysis of 16S rRNA gene reveals that strain CWC-01^T is most closely related to Methanobacterium petrolearium Mic5c12^T, with 96.63% identity. Genome size of strain CWC-01^T is 1.98 Mb and it is the smallest genome size of genus. The genomic DNA G+C content obtained from the genome sequence of strain CWC-01^T is 44.15 mol%. Based on these phenotypic, phylogenetic and genomic analyses, we propose that strain CWC-01^T represents a novel species in genus Methanobacterium, for which the name Methanobacterium aridiramus sp. nov. is proposed. The type strain is CWC-01^T (=BCRC AR10053^T=NBRC 113991^T).