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

A marine bacterial strain, named NTOU-MSR1^T, was isolated from marine sediment of northern coast of Taiwan. This bacterium was Gram-stain-negative, aerobic, and motile, with a single flagellum. Its rod-shaped cells measured approximately 0.5-0.6 µm in width and 1.8-2.0 μm in length. NTOU-MSR1^T grew at temperatures ranging from 10 to 45 °C, optimally at 30 °C. The pH range for growth was 7.0-10.0, with optimal growth at pH 7.0-8.0. It tolerated NaCl concentrations up to 12%. The cell membrane predominantly contained fatty acids such C_16:1ω7c, C_18:1ω7c, and C_16:0. The overall genome relatedness indices indicated that strain NTOU-MSR1^T had an average nucleotide identity (ANI) of 87.88% and a digital DNA-DNA hybridization (dDDH) value of 35.40% compared to its closest related species, O. marisflavi 102-Na3^T. These values fell below the 95% and 70% threshold for species delineation, respectively. These findings suggested that the strain NTOU-MSR1^T was a new member of the Oceanimonas genus. Its genomic DNA had a G + C content of 61.0 mol%. Genomic analysis revealed genes associated with the catechol branch of β- ketoadipate pathway for degrading polycyclic aromatic hydrocarbons, resistance to heavy metal, biosynthesis of polyhydroxybutyrate and the production of glycoside hydrolases (GH19, GH23, and GH103) for chitin and glycan digestion. Additionally, NTOU-MSR1^T was capable of synthesizing biosurfactants and potentially degrading plastic. The proposed name for this new species is Oceanimonas pelagia, with the type strain designated as NTOU-MSR1^T (= BCRC 81403^T = JCM 36023^T).

Strain AA17^T was isolated from an apparently healthy fragment of Montipora capitata coral from the reef surrounding Moku o Lo'e in Kāne'ohe Bay, O'ahu, Hawai'i, USA, and was taxonomically evaluated using a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain AA17^T shared the greatest similarity with Aestuariibacter halophilus JC2043^T (96.6%), and phylogenies based on 16S rRNA gene sequences grouped strain AA17^T with members of the Aliiglaciecola, Aestuariibacter, Lacimicrobium, Marisediminitalea, Planctobacterium, and Saliniradius genera. To more precisely infer the taxonomy of strain AA17^T, a phylogenomic analysis was conducted and indicated that strain AA17^T formed a monophyletic clade with A. halophilus JC2043^T, divergent from Aestuariibacter salexigens JC2042^T and other related genera. As a result of monophyly and multiple genomic metrics of genus demarcation, strain AA17^T and A. halophilus JC2043^T comprise a distinct genus for which the name Fluctibacter gen. nov. is proposed. Based on a polyphasic characterisation and identifying differences in genomic and taxonomic data, strain AA17^T represents a novel species, for which the name Fluctibacter corallii sp. nov. is proposed. The type strain is AA17^T (= LMG 32603 ^T = NCTC 14664^T). This work also supports the reclassification of A. halophilus as Fluctibacter halophilus comb. nov., which is the type species of the Fluctibacter genus. Genomic analyses also support the reclassification of Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica.

Desulfofundulus kuznetsovii is a thermophilic, spore-forming sulphate-reducing bacterium in the family Peptococcaceae. In this study, we describe a newly isolated strain of D. kuznetsovii, strain TPOSR, and compare its metabolism to the type strain D. kuznetsovii 17^T. Both strains grow on a large variety of alcohols, such as methanol, ethanol and propane-diols, coupled to the reduction of sulphate. Strain 17^T metabolizes methanol via two routes, one involving a cobalt-dependent methyl transferase and the other using a cobalt-independent alcohol dehydrogenase. However, strain TPOSR, which shares 97% average nucleotide identity with D. kuznetsovii strain 17^T, lacks several genes from the methyl transferase operon found in strain 17^T. The gene encoding the catalytically active methyl transferase subunit B is missing, indicating that strain TPOSR utilizes the alcohol dehydrogenase pathway exclusively. Both strains grew with methanol during cobalt starvation, but growth was impaired. Strain 17^T was more sensitive to cobalt deficiency, due to the repression of its methyl transferase system. Our findings shed light on the metabolic diversity of D. kuznetsovii and their metabolic differences of encoding one or two routes for the conversion of methanol.

A gram-stain-positive, aerobic, rod-shaped bacterial strain capable of producing siderophores, named YIM B08730^T, was isolated from a soil sample collected from Wumeng Mountain National Nature Reserve, Zhaotong City, Yunnan Province. Growth occurred at 10-45 °C (optimum, 35-40 ℃), pH 7.0-9.0 (optimum, 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 0-1 %, w/v). A comparative analysis of the 16S rRNA gene sequence (1558 bp) of strain YIM B08730^T showed the highest similarity to Solibacillus isronensis JCM 13838^T (96.2 %), followed by Solibacillus silvestris DSM 12223^T (96.0 %) and Solibacillus kalamii ISSFR-015^T (95.4 %). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unidentified lipid. The main respiratory quinone of strain YIM B08730^T was menaquinone 7 (MK-7). The major fatty acids were iso-C_15:0 and C_16:1ω7c alcohol. The digital DNA-DNA hybridization and average nucleotide identity values between strain YIM B08730^T and the reference strain S. isronensis JCM 13838^T were 24.8 % and 81.2 %, respectively. The G + C content of the genomic DNA was 37.1 mol%. The genome of the novel strain contained genes associated with the production of siderophores, and it also revealed other functional gene clusters involved in plant growth promotion and soil bioremediation. Based on these phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM B08730^T is considered to be a novel species of the genus Solibacillus, for which the name Solibacillus ferritrahens sp. nov. is proposed. The type strain is YIM B08730^T (= NBRC 116268^T = CGMCC 1.60169^T).

The fast-growing rhizobia-like strains S101^T and S153, isolated from root nodules of soybean (Glycine max) in Sichuan, People's Republic of China, underwent characterization using a polyphasic taxonomy approach. The strains exhibited growth at 20-40 °C (optimum, 28 °C), pH 4.0-10.0 (optimum, pH 7.0) and up to 2.0% (w/v) NaCl (optimum, 0.01%) on Yeast Mannitol Agar plates. The 16S rRNA gene of strain S101^T showed 98.4% sequence similarity to the closest type strain, Ciceribacter daejeonense L61^T. Major cellular fatty acids in strain S101^T included summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_19:0 cyclo ω8c. The predominant quinone was ubiquinone-10. The polar lipids of strain S101^T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethyl ethanolamine, phosphatidyl ethanolamine, amino phospholipid, unidentified phosphoglycolipid and unidentified amino-containing lipids. The DNA G + C contents of S101^T and S153 were 61.1 and 61.3 mol%, respectively. Digital DNA-DNA hybridization relatedness and average nucleotide identity values between S101^T and C. daejeonense L61^T were 46.2% and 91.4-92.2%, respectively. In addition, strain S101^T promoted the growth of soybean and carried nitrogen fixation genes in its genome, hinting at potential applications in sustainable agriculture. We propose that strains S101^T and S153 represent a novel species, named Ciceribacter sichuanensis sp. nov., with strain S101^T as the type strain (= CGMCC 1.61309 ^T = JCM 35649 ^T).

Two fungal strains (K-2^T and S1) were isolated from the deepest ocean sediment of the Challenger Deep located in the Mariana Trench. The internal transcribed spacer (ITS) gene sequences of the isolates K-2^T and S1 differed from those of closely related species, such as Talaromyces assiutensis and T. trachyspermus. Phylogenetic analyses based on single and concatenated alignments of the genes, namely ITS, β-tubulin (benA), calmodulin (cam), and the second-largest subunit fragment of the RNA polymerase II (rpb2) showed that the isolates K-2^T and S1 were clustered together with other Talaromyces species, such as T. trachyspermus and T. assiutensis, as evidenced by the position on a terminal branch with high bootstrap support. They could also be distinguished from their closest relatives with valid published names via morphological and physiological characteristics, for example, growth at 4 °C-50 °C with a pH in the range of 1.5-12. Based on their phylogenetic, morphological, and physicochemical properties, the isolates K-2^T and S1 represent a novel species in the genus Talaromyces, and the proposed name is Talaromyces sedimenticola sp. nov. The type strain is K-2^T (= GDMCC 3.746^T = JCM 39451^T).

Pleurotus tuber-regium (Fr.) Sing. can evade oxygen by forming sclerotia under oxidative stress, consequently averting the development of hyperoxidative state, during which the expression level of catalase gene (PtCat) is significantly up-regulated. To investigate the relationship between the catalase gene and sclerotia formation, over-expression and interference strains of the PtCat gene were obtained by Agrobacterium tumefaciens-mediated transformation for phenotypic analysis. In the absence of hydrogen peroxide (H₂O₂) stress, a minor difference was observed in the mycelial growth rate and the activity of antioxidant enzymes between the over-expression and interference strains. However, when exposed to 1-2 mM H₂O₂, the colony diameter of the over-expression strain was approximately 2-3× that of the interference strain after 8 days of culturing. The catalase activity of the over-expression strain increased by 1000 U/g under 2 mM H₂O₂ stress, while the interference strain increased by only 250 U/g. After one month of cultivation, the interference strain formed an oval sclerotium measuring 3.5 cm on the long axis and 2 cm on the short axis, while the over-expression strain did not form sclerotia. Therefore, it is concluded that catalase activity regulates the formation of sclerotia in P. tuber-regium.

As part of a long-term study aiming to isolate and identify yeast species that inhabit the surface of leaves and fruits of native fine-aroma cacao in the department of Amazonas, Peru, we obtained multiple isolates of Hannaella species. Yeasts of the genus Hannaella are common inhabitants of the phyllosphere of natural and crop plants. On the basis of morphological, and physiological characteristics, and sequence analysis of the D1/D2 domains of the large subunit rRNA gene (LSU) and the internal transcribed spacer region (ITS), we identified five species of Hannaella from the phyllosphere of Peruvian cacao. Four have been previously described: H. phyllophila (isolates KLG-073, KLG-091), H. pagnoccae (KLG-076), H. sinensis (KLG-121), and H. taiwanensis (KLG-021). A fifth, represented by eight isolates (KLG-034, KLG-063, KLG-074, KLG-078, KLG-79, KLG-082, KLG-084, KLG-085), is not conspecific with any previously described Hannaella species, and forms the sister clade to H. surugaensis in the phylogenetic analysis. It has 2.6-3.9% (18-27 substitutions, 2-4 deletions, and 1-3 insertions in 610-938 bp-long alignments), and 9.8-10.0% nucleotide differences (37 substitutions and 14 insertions in 511-520 bp-long alignments) in the LSU and ITS regions, respectively, to H. surugaensis type strain, CBS 9426. Herein, the new species Hannaella theobromatis sp. nov. is described and characterised. The species epithet refers to its epiphytic ecology on its host Theobroma cacao.

In the search of new enzymatic activities with a possible industrial application, we focused on those microorganisms and their molecular mechanisms that allow them to succeed in the environment, particularly in the proteolytic activity and its central role in the microorganisms' successful permanence. The use of highly active serine proteases for industrial applications is a modern need, especially for the formulation of detergents, protein processing, and hair removal from animal skins. This report provides the isolation and identification of a highly proteolytic fragment derived from DegQ produced by a Pseudomonas fluorescens environmental strain isolated from a frog carcass. Zymograms demonstrate that a 10 kDa protein mainly generates the total proteolytic activity of this strain, which is enhanced by the detergent SDS. Mass spectroscopy analysis revealed that the protein derived a couple of peptides, the ones showing the highest coverage belonging to DegQ. Interestingly, this small protein fragment contains a PDZ domain but no obvious residues indicating that it is a protease. Protein model analysis shows that this fragment corresponds to the main PDZ domain from DegQ, and its unique sequence and structure render a proteolytic peptide. The results presented here indicate that a novel DegQ fragment is sufficient for obtaining high protease activity highlighting that the analysis of environmental microorganisms can render new strains or enzymes with helpful biotechnological characteristics.

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.