Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

A Gram-stain-negative bacterium, designated as strain TK19100^T, was isolated from the mid-ridge of the Southwest Indian Ocean. Cells of strain TK19100^T were strictly aerobic, non-motile and short-rod shaped with fimbriae-like structures around the cell surface. Growth occurred at 15–40 °C, at pH 6.0–9.0 and with 1–10% (w/v) NaCl. Strain TK19100^T shared the highest 16S rRNA gene sequence similarity with Cerasicoccus frondis NBRC 105381^T of 97.74%, followed by Cerasicoccus arenae KCTC 12870^T of 97.69% and Cerasicoccus maritimus NBRC 105382^T of 97.40%. The phylogenetic tree based on both 16S rRNA genes and 92 core genes placed strain TK19100^T in a new linage within the genus Cerasicoccus. The genome size of strain TK19100^T was 5.07 Mb with the DNA G + C content 56.1%. The average nucleotide identity value and the digital DNA-DNA hybridization value of strain TK19100^T compared with the closest related species, Cerasicoccus frondis, were 78.39% and 23.70%, respectively. Strain TK19100^T encoded a previously unreported combination of GH16 and Carbohydrate Binding Module 96. The major fatty acids of strain TK19100^T were C_14:0 and C_18:1 ω9c. Menaquinone-7 was the sole respiratory quinone. The phenotypic and genotypic characterization analysis indicate that strain TK19100^T represents a novel species affiliated to the genus Cerasicoccus, for which the name Cerasicoccus fimbriatus sp. nov. is proposed. The type strain is TK19100^T (= CGMCC 1.18957^T = NBRC 116189^T).

A Gram-stain-negative, non-motile, aerobic, pale-yellow coloured and oval-shaped bacterium designated GRR-S6-38^T was isolated from a tidal flat sediment that collected from Garorim Bay of the Yellow Sea, Republic of Korea. Strain GRR-S6-38^T grew at 15–40 °C (optimum, 30 °C) at pH 6–9 (optimum, pH 7) and at 2–6% (w/v) NaCl (optimum, 2% NaCl). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GRR-S6-38^T was closely related to those of J. seosinensis CL-SP26^T (98.1%), J. helgolandensis DSM 14858^T (97.4%), J. rubra CECT 5088^T (97.4%), J. faecimaris DSM 100420^T (97.4%), J. marina SHC163T (97.3%), J. donghaensis CECT 7802^T (97.2%) and J. pohangensis DSM 19073^T (97.1%). The average nucleotide identity and digital DNA-DNA hybridization value between GRR-S6-38^T and related type strains were 71.47–78.59% and 17.80–21.40%. Strain GRR-S6-38^T was characterized as having Q-10 as the predominant respiratory quinone and the major principle fatty acids (> 10%) were SF 8 (C_18:1 ω7c/C_18:1 ω6c, 39.3%), C_19:0 ω8c cyclo (13.2%) and C_18:1 ω7c 11-methyl (10.6%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified lipid, two unidentified aminolipids and two unidentified phospholipids. The assembled genome of strain GRR-S6-38^T has a total length of 3.32 Mbp, and a G + C content is 69.98%. Based on the polyphasic taxonomic evidence presented in this study, GRR-S6-38^T is regarded to represent a novel species within the genus Jannaschia, for which name Jannaschia ovalis sp. nov. is proposed. The type strain is GRR-S6-38^T (= KCTC 82518 = KACC 22240 = JCM 36187).

The underexplored halophilic genus Joostella within the Flavobacteriaceae family consists of only two species, both of which have received little attention for their potential biotechnological applications. In this study, we report the isolation and characterisation of a novel halophilic bacterium, strain CR20, using a genomic approach to investigate its biotechnological potential. Analysis of the 16S rRNA gene revealed that strain CR20 shares 97.5% and 96.2% sequence similarity with Joostella marina DSM 19592 ^T and Joostella atrarenae M1-2 ^T, respectively. Strain CR20 exhibited average nucleotide identity and digital DNA-DNA hybridisation values of 76.8–79.1% and 20.8–22.8%, respectively, with Joostella spp., which fall below the species delineation thresholds. Additionally, strain CR20 demonstrated average amino acid identity and percentage of conserved proteins values of 81.3–84.0% and 71.7–75.3%, respectively, with Joostella spp., above the genus delineation thresholds. Meanwhile, the average amino acid identity and percentage of conserved proteins values of strain CR20 against Galbibacter spp. are 73.9–80.0% and 61.3–72.3%, respectively, also above the genus delineation thresholds. These findings indicated strain CR20 has a close relationship with both genera. Chemotaxonomic analysis of strain CR20 identified predominant fatty acids, including iso-C_17:0 3OH (25.3%), iso-C_15:0 (14%), and C_16:1 ω6c/C_16:1 ω7c (12.2%). The assembled genome comprises 62 contigs, with a size of approximately 3,168,727 bp and a G + C content of 35.1%. Among 2,804 predicted genes, 2,559 were classified into 25 COG functional groups. A total of 68 genes with potential industrial applications were identified, including 1 β-mannanase, 2 β-xylosidases, 1 polysaccharide deacetylase, 4 other hemicellulases, 6 β-glucosidases, 25 proteases, and 29 phosphate-solubilising enzymes. Hydrolytic assays confirmed that strain CR20 produces these enzymes extracellularly. These findings highlight strain CR20 has potential for industrial applications.

A bacterial strain, REN37^T, was isolated from fermented grains of Baijiu samples collected from Sichuan, PR China. The cells of strain REN37^T was Gram-negative and aerobic. The cellular morphology exhibited rod-shaped cells without flagellum, displaying non-motility. The optimal growth condition was at 32–37 °C, pH 6.0–7.0, and with a NaCl concentration of 1–2% (w/v). Based on the analysis of 16S rRNA gene sequence, strain REN37^T was identified to belong to the genus of Isoalcanivorax. Its closest species was Isoalcanivorax pacificus W11-5 ^T (96.1%). The polar lipids were identified to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified glycolipid, two unidentified phospholipids. The predominant menaquinone was MK-12. The predominant fatty acids were C_15:0 anteiso (49.4%), C_16:0 iso (18.1%), C_17:0 anteiso (16.5%) and C_15:0 iso (9.5%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (OrthoANI) and average amino acid identify (AAI) values between strain REN37^T and its most similar species were 19.2%, 74.0% and 78.0%, respectively. The DNA G + C content of the strain REN37^T was 63.0 mol%. Three alkane 1-monooxygenase (alkB1) genes (1152 bp, 1149 bp, 1179 bp) were identified in the genome, indicating that strain REN37^T may be associated with efficient oil-degradation capabilities. Based on the results, REN37^T represents a novel specie, and the name Isoalcanivorax beigongshangi sp. nov. was proposed. The type strain is REN37^T (= GDMCC 1.3120 ^T = JCM 35319 ^T).

A novel gram-stain-indeterminate, rod-shaped, endospore-forming, motile, aerobic bacterium, designated JETA1-E2^T, was isolated from aircraft fuel Jet A1 sample. The strain showed high pairwise similarity values of partial 16S rRNA gene sequences to Sphingomonas paucimobilis (MT367853) (99.42%), Sphingomonas sanguinis (MF319771) (99.34%), and Sphingomonas pseudosanguinis (HE716953) (99.27%) within the family Sphingomonadaceae. However, API test results revealed that the strain JETA1-E2^T differed from these type strains. The phylogenetic tree based on the whole genome and the phylogenomic tree generated with the UBCG tool showed that the strain JETA1-E2^T formed a distinct monophyletic clade within the family Sphingomonadaceae, and clustered distantly with the genera Sphingomonas and Sphingobium. The predominant respiratory quinone is Q-10. The major fatty acids are C_16:0 and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). C_19:0 is present in small amounts. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, aminophospholipid, unidentified glycolipid, and two unidentified sphingoglycolipids. The only polyamine is putrescine in minor amounts. The DNA G + C content of the type strain is 66.5 mol%. Several unique genes in the strain JETA1-E2^T may contribute to fight against various stressors, virulence and pathogenicity, as well as survival in challenging conditions. The strain JETA1-E2^T contains 100 of the characterised proteins available in the HADEG database of which 58% of these are involved in metabolic process of aromatics degradation. The findings indicate that the strain JETA1-E2^T has the potential to metabolise hydrocarbons such as fuel, especially aromatic compounds. Based on the results of polyphasic taxonomic analyses, the strain JETA1-E2^T represents a novel species in a new genus in the family Sphingomonadaceae for which the name Facivitalis istanbulensis gen. nov., sp. nov. is proposed. The type strain of Facivitalis istanbulensis is JETA1-E2^T (DSM 117971^T = LMG 33634^T = KUEN 1206 (B) F3-1-1^T).

On the deep and dark seafloor, a cryptic and yet untapped microbial diversity flourishes around hydrothermal vent systems. This remote environment of difficult accessibility exhibits extreme conditions, including high pressure, steep temperature- and redox gradients, limited availability of oxygen and complete darkness. In this study, we analysed the genomes of three aerobic strains belonging to the phylum Planctomycetota that were isolated from two deep-sea iron- rich hydroxide deposits with low temperature diffusive vents. The vents are located in the Arctic and Pacific Ocean at a depth of 600 and 1,734 m below sea level, respectively. The isolated strains Pr1d^T, K2D and TBK1r were analyzed with a focus on genome-encoded features that allow phenotypical adaptations to the low temperature iron-rich deep-sea environment. The comparison with genomes of closely related surface-inhabiting counterparts indicates that the deep-sea isolates do not differ significantly from members of the phylum Planctomycetota inhabiting other habitats, such as macroalgae biofilms and the ocean surface waters. Despite inhabiting extreme environments, our “deep and dark”-strains revealed a mostly non-extreme genome biology.

Two novel strains, SYSU D00514^T and SYSU D00778, were isolated from desert soil in the Gurbantunggut Desert, Xinjiang Uygur Autonomous Regions, PR China. SYSU D00514^T and SYSU D00778 were aerobic, Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative. SYSU D00514^T grew at temperatures ranging from 4 to 37 °C (optimum, 28–30 °C), at pH 6.0–8.0 (optimum, 7.0), and tolerated NaCl concentrations from 0 to 7.5% (optimum, 0.5% w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains SYSU D00514^T and SYSU D00778 were closely related to the members of the genus Nocardioides. Two isolates were most closely related to Nocardioides alpinus Cr7-14 ^T (98.05% and 98.19%). The G + C content of the genomic DNA of strains SYSU D00514^T and SYSU D00778 were both 72.8%. Strain SYSU D00514^T and the type strains of the genus Nocardioides in the analysis had average nucleotide identity values of 76.8–85.8% as well as digital DNA–DNA hybridization values between 19.5% and 28.0%. The predominant cellular fatty acids of strain SYSU D00514^T were C_17:1 ω8c, C_18:1 ω9c and iso-C_16:0. For strain SYSU D00514^T, the major polar lipids encompassed diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, an unidentified aminophospholipid and two unidentified aminolipids. The main respiratory quinone of strain SYSU D00514^T was MK-8 (H4). Based on the results of polyphasic taxonomic experiments, we propose that strains SYSU D00514^T and SYSU D00778 represent a novel species of the genus Nocardioides, with the name Nocardioides xinjiangensis. The type strain is SYSU D00514^T (= CGMCC 1.18622 ^T = MCCC 1K05001^T = KCTC 49488 ^T).

A Gram-positive, moderately halophilic, rod-shaped and facultatively anaerobic strain T66^T, was isolated from the rhizosphere soil of mangrove Acanthus ebracteatus in Guangxi, China. Strain T66^T was observed to grow at 15–40 ℃ (optimum 30 ℃), pH 5–8 (optimum 6–7) and with 2–20% (w/v) NaCl (optimum 6%). The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain T66^T to be closely related to Halobacillus litoralis SL-4 ^T (98.72%), Halobacillus dabanensis D-8 ^T (98.70%) and Halobacillus campisalis ASL-17 ^T (98.66%). The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain T66^T belonged to the genus Halobacillus and formed a separate branch. The digital DNA-DNA hybridisation and average nucleotide identify values between strain T66^T and its related species were 17.80–19.80% and 70.78–73.22%, respectively, which were lower than the threshold recommended for species delineation. The genomic DNA G + C content was 40.9%. The predominant isoprenoid quinone was MK-7, the cell-wall peptidoglycan contained meso-diaminopimelic acid, and the major fatty acids that accounted for more than 10.0% were anteiso-C_15:0 (68.4%) and anteiso-C_17:0 (13.4%). Phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid were found in the polar lipid extraction. Strain T66^T could hydrolyse casein and contains several genes (e. g. vanY, vpr, pbpG and elpC) involved in protease. Therefore, strain T66^T is salt-tolerant and produces protease, and it may have development and utilisation value in flavouring agents and food curing. Based on phenotypic, chemotaxonomic data and genotypic characteristics, strain T66^T represents a novel species of the genus Halobacillus, for which the name Halobacillus rhizosphaerae sp. nov. is proposed. The type strain is T66^T (= JCM 36534 ^T = MCCC 1K08701^T).

Mycobacteroides abscessus is a non-tuberculous mycobacteria implicated in causing lung infections. It is difficult to control owing to resistance to antibiotics and disinfectants. This work was aimed at comprehending: the pan-genome architecture, evolutionary dynamics, and functionalities of pan-genome components linked to COGs and KEGG. Around 2802 core genes were present in each strain of the M. abscessus genome. The number of accessory genes ranged from 1615 to 2481. The open pan-genome of M. abscessus was attributed to the accessory genes underlining its adaptability in the host. Phylogenetic analysis revealed cluster-based relationships and highlighted factors shaping variability and adaptive capabilities. Transcription, metabolism, and pathogenic genes were vital for M. abscessus lifestyle. The accessory genes contributed to the diverse metabolic capability. The incidence of a significant portion of secondary metabolite biosynthesis genes provided insights for investigating their biosynthetic gene clusters. Additionally, a high proportion of xenobiotic biodegradation genes highlighted potential metabolic capabilities. In silico screening identified a potential vaccine candidate among hypothetical proteins in COGs. Functional analysis of M. abscessus pan-genome components unveiled factors associated with virulence, pathogenicity, infection establishment, persistence, and resistance. Notable amongst them were: MMPL family transporters, PE-PPE domain-containing proteins, TetR family transcriptional regulators, ABC transporters, Type—I, II, III, VII secretion proteins, DUF domain-containing proteins, cytochrome P450, VapC family toxin, virulence factor Mce family protein, type II toxin-antitoxin system. Overall, these results enhanced understanding of the metabolism, host–pathogen dynamics, pathogenic lifestyle, and adaptations. This will facilitate further investigations for combating infections and designing suitable therapies.

A novel methanotrophic strain 9N^T was isolated from the sludge of a freshwater lake. Cells were aerobic, Gram-stain-negative, non-motile pleomorphic rods with intracytoplasmic membrane systems that appropriate type-II methanotrophs and hemispherical and spherical exocellular formations on the perimeter of the cell wall surface. The novel isolate grows only on methane or methanol as the sole carbon and energy source, at 10–37 °C (optimum 28–30 °C), pH 4.5–9.0 (optimum 7.0–7.5), up to 1% NaCl (optimum 0.3–0.5%). Methanol supported the growth of the strain 9N^T in a wide range of concentrations from 0.05 to 5.0% (v/v) with an optimum of 0.5% (v/v). The major fatty acids were C_18:1ω8c and C_18:1ω7c. Based on 16S rRNA gene sequence phylogenetic analysis, strain 9N^T was closely related to representatives of the genus Methylocystis (96.5–98.3%). The genome of strain 9N^T was 3.34 Mbp in size with 63.5% of G + C content. The average nucleotide identity and digital DNA–DNA hybridization values between strain 9N^T and closely related type strains of genus Methylocystis were 78.0–82.4% and 20.9–24.3%, respectively. The careful genome annotation of the novel strain shows it possessed genes for the detoxification of arsenate and cyanides as well as genes potentially involved in plant growth promotion (such as biosynthesis of indoles, cytokinins, polyhydroxybutyrate, siderophore production, and nitrogen fixation). Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Methylocystis borbori sp. nov. as novel species of the genus Methylocystis. The type strain is 9N^T (= VKM B-3616^T = KCTC 92566^T).