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

The decline of new antibiotics and the emergence of multidrug resistance in pathogens necessitates a revisit of strategies used for lead compound discovery. This study proposes to induce the production of bioactive compounds with sub-lethal concentrations of silver nanoparticles (Ag-NPs). A total of Forty-two Actinobacteria isolates from four Saudi soil samples were grown with and without sub-lethal concentration of Ag-NPs (50 µg ml⁻¹). The spent broth grown with Ag-NPs, or without Ag-NPs were screened for antimicrobial activity against four bacteria. Interestingly, out of 42 strains, broths of three strains grown with sub-lethal concentration of Ag-NPs exhibit antimicrobial activity against Staphylococcus aureus and Micrococcus luteus. Among these, two strains S4-4 and S4-21 identified as Streptomyces labedae and Streptomyces tirandamycinicus based on 16S rRNA gene sequence were selected for detailed study. The change in the secondary metabolites profile in the presence of Ag-NPs was evaluated using GC–MS and LC–MS analyses. Butanol extracts of spent broth grown with Ag-NPs exhibit strong antimicrobial activity against M. luteus and S. aureus. While the extracts of the controls with the same concentration of Ag-NPs do not show any activity. GC-analysis revealed a clear change in the secondary metabolite profile when grown with Ag-NPs. Similarly, the LC–MS patterns also differ significantly. Results of this study, strongly suggest that sub-lethal concentrations of Ag-NPs influence the production of secondary metabolites by Streptomyces. Besides, LC–MS results identified possible secondary metabolites, associated with oxidative stress and antimicrobial activities. This strategy can be used to possibly induce cryptic biosynthetic gene clusters for the discovery of new lead compounds.

The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H₂, indicating that besides H₂S, H₂ could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H₂S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.

A Gram-negative, rod-shaped, non-motile, aerobic bacterium, designated as strain TK19101^T, was isolated from the intermediate seawater of yellow vent in the shallow-sea hydrothermal system located near Kueishantao Island. The strain was found to grow at 10–40 °C (optimum, 35 °C), at pH 6.0–8.0 (optimum, 7.0), and in 0–5% (w/v) NaCl (optimum, 1%). Strain TK19101^T was catalase-positive and oxidase-positive. The predominant fatty acids (> 10%) in strain TK19101^T cells were C_16:0, summed feature 8 (C_18:1 ω6c and/or C_18:1 ω7c), and C_18:0. The predominant isoprenoid quinone of strain TK19101^T was ubiquinone-10. The polar lipids of strain TK19101^T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and unknown polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TK19101^T belonged to the genus Mesobacterium. Strain TK19101^T exhibited highest 16S rRNA gene sequence similarity value to Mesobacterium pallidum MCCC M24557^T (97.48%). The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain TK19101^T and the closest related species Mesobacterium pallidum MCCC M24557^T were 74.88% and 20.30%, respectively. The DNA G + C content was 63.49 mol%. On the basis of the analysis of 16S rRNA gene sequences, genotypic and phylogenetic data, strain TK19101^T has a unique phylogenetic status and represents a novel species of genus Mesobacterium, for which the name Mesobacterium hydrothermale sp. nov. is proposed. The type strain is TK19101^T (= MCCC 1K08936^T = KCTC 8354^T).

Biological control is a promising approach to enhance pathogen and pest control to ensure high productivity in cash crop production. Therefore, PGPR biofertilizers are very suitable for application in the cultivation of tea plants (Camellia sinensis) and tobacco, but it is rarely reported so far. In this study, production of a consortium of three strains of PGPR were applied to tobacco and tea plants. The results demonstrated that plants treated with PGPR exhibited enhanced resistance against the bacterial pathogen Pseudomonas syringae (PstDC3000). The significant effect in improving the plant's ability to resist pathogen invasion was verified through measurements of oxygen activity, bacterial colony counts, and expression levels of resistance-related genes (NPR1, PR1, JAZ1, POD etc.). Moreover, the application of PGPR in the tea plantation showed significantly reduced population occurrences of tea green leafhoppers (Empoasca onukii Matsuda), tea thrips (Thysanoptera:Thripidae), Aleurocanthus spiniferus (Quaintanca) and alleviated anthracnose disease in tea seedlings. Therefore, PGPR biofertilizers may serve as a viable biological control method to improve tobacco and tea plant yield and quality. Our findings revealed part of the mechanism by which PGPR helped improve plant biostresses resistance, enabling better application in agricultural production.

A Gram-stain-negative, facultative anaerobe, rod-shaped strain JX-1^T was isolated from UASB sludge treating landfill leachate in Wuhan, China. The isolate is capable of growing under conditions of pH 6.0–11.0 (optimum, pH 7.0–8.0), temperature 4–42 ℃ (optimum, 20–30 ℃), 0–8.0% (w/v) NaCl (optimum, 5.0%), and ammonia nitrogen concentration of 200–5000 mg/L (optimum, 500 mg/L) on LB plates. The microorganism can utilize malic acid, D-galactose, L-rhamnose, inosine, and L-glutamic acid as carbon sources, but does not reduce nitrates and nitrites. The major fatty acids are C_18:1ω7c/C_18:1ω6c, iso-C_15:0, and anteiso-C_15:0. The respiratory quinones are Q9 (91.92%) and Q8 (8.08%). Polar lipids include aminolipid, aminophospholipid, diphosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Compared with other strains, strain JX-1^T and Denitrificimonas caeni HY-14^T have the highest values in terms of 16S rRNA gene sequence similarity (96.79%), average nucleotide identity (ANI; 76.06%), and average amino acid identity (AAI; 78.89%). Its digital DNA-DNA hybridization (dDDH) result is 20.3%. The genome of strain JX-1^T, with a size of 2.78 Mb and 46.12 mol% G + C content, lacks genes for denitrification and dissimilatory nitrate reduction to ammonium (DNRA), but contains genes for ectoine synthesis as a secondary metabolite. The results of this polyphasic study allow genotypic and phenotypic differentiation of the analysed strain from the closest related species and confirm that the strain represents a novel species within the genus Denitrificimonas, for which the name Denitrificimonas halotolerans sp. nov. is proposed with JX-1^T (= MCCC 1K08958^T = KCTC 8395^T) as the type strain.

Strain MP-1014^T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97–99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014^T exhibits the highest similarity to I. sediminis JC619^T (99.7%), I. chiayiensis KCTC19740^T (98.9%), and subsequently to I. halotolerans KCTC19646^T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014^T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619^T, I. chiayiensis KCTC19740^T and I. halotolerans KCTC19646^T respectively. The major polar lipids of the strain MP-1014^T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK₉ (H₄) and MK₉ (H₂). The major fatty acids were anteiso-C_15:0, anteiso-C_17:0, iso-C_14:0, C_15:0, and C_16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 ^T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 ^T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014^T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646^T; DSMZ = 29325^T; MTCC = 13246^T].

Two alkaliphilic, Gram‐stain-negative bacterial strains (MEB004^T and MEB108^T) were isolated from water samples collected from Lonar lake, India. The phylogenetic analysis of their 16S rRNA gene sequences showed the highest similarity to A. delamerensis DSM 18314^T (98.4%), followed by A. amylolytica DSM 18337^T and A. collagenimarina JCM 14267^T (97.9%). The genome sizes of strains MEB004^T and MEB108^T were determined to be 3,858,702 and 4,029,814 bp, respectively, with genomic DNA G + C contents of 51.4 and 51.9%. Average Nucleotide Identity, DNA–DNA Hybridization and Amino Acid Identity values between strains (MEB004^T and MEB108^T) and A. amylolytica DSM 18337^T were (82.3 and 85.5), (25.0 and 29.2) and (86.7 and 90.2%). Both novel strains produced industrially important enzymes, such as amylase, lipase, cellulase, caseinase, and chitinase at pH 10 evidenced by the genomic presence of carbohydrate-active enzymes encoding genes. Genomic analyses further identified pH tolerance genes, affirming their adaptation to alkaline Lonar Lake. Dominant fatty acids were Summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), C_16:0, Summed feature 3, Sum In Feature 2 and C_12:0 3OH. The prevalent polar lipids included phosphatidyl ethanolamine, phosphatidyl glycerol, and diphosphatidyl glycerol. The major respiratory quinone was ubiquinone-8. Based on the polyphasic data, we propose the classification of strains MEB004^T and MEB108^T as novel species within the genus Alkalimonas assigning the names Alkalimonas mucilaginosa sp. nov. and Alkalimonas cellulosilytica sp. nov., respectively. The type strains are MEB004^T (= MCC 5208^T = JCM 35954^T = NCIMB 15460^T) and MEB108^T (= MCC 5330^T = JCM 35955^T = NCIMB 15461^T).

Two novel Gram-stain-negative strains designated P7^T and P8^T, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species within the genus Roseateles through a polyphasic taxonomic approach. These aerobic, rod-shaped, non-sporulating strains demonstrated optimal growth at 30 °C, pH 7, and in the absence of NaCl (0% w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated close relationships with Roseateles saccharophilus DSM654^T (98.7%) and Roseateles puraquae CCUG 52769^T (98.96%), respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the isolates with the most closely related strains with publicly available whole genomes were 82.0–85.5% and 25.0–30.2%, respectively. The predominant fatty acids identified were C_16:0 and summed feature 3 (composed of C_16:1 ω6c and/or C_16:1 ω7c), with minor amounts of C_12:0, C_10:0 3–OH and summed feature 8 (composed of C_18:1 ω7c and/or C_18:1 ω6c; 26.4%). Ubiquinone 8 was the main quinone, and the polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, two unidentified phosphoaminolipids, one unidentified phosphoglycolipid, three unidentified phospholipids, and one unidentified aminolipid. The draft genome sequences revealed genomic DNA G + C contents of 70.1% for P7^T and 68.2% for P8^T. Comprehensive physiological, biochemical, and 16S rRNA sequence analyses confirm these isolates as novel species of the genus Roseateles, proposed to be named Roseateles caseinilyticus sp. nov for strain P7^T (= KACC 22504^T = TBRC 15694^T) and Roseateles cellulosilyticus sp. nov. for strain P8^T (= KACC 22505^T = TBRC 15695^T).

Yersinia is an important genus comprising foodborne, zoonotic and pathogenic bacteria. On the other hand, species of the so-called group Yersinia enterocolitica-like are understudied and mostly characterized as non-pathogenic, despite of some reports of human infections. The present study aimed to provide genomic insights of Yersinia frederiksenii (YF), Yersinia intermedia (YI) and Yersinia kristensenii (YK) isolated worldwide. A total of 22 YF, 20 YI and 14 YK genomes were searched for antimicrobial resistance genes, plasmids, prophages, and virulence factors. Their phylogenomic relatedness was analyzed by Gegenees and core-genome multi-locus sequence typing. Beta-lactam resistance gene bla_TEM-116 and five plasmids replicons (pYE854, ColRNAI, ColE10, Col(pHAD28) and IncN3) were detected in less than five genomes. A total of 59 prophages, 106 virulence markers of the Yersinia genus, associated to adherence, antiphagocytosis, exoenzymes, invasion, iron uptake, proteases, secretion systems and the O-antigen, and virulence factors associated to other 20 bacterial genera were detected. Phylogenomic analysis revealed high inter-species distinction and four highly diverse YF clusters. In conclusion, the results obtained through the analyses of YF, YI and YK genomes suggest the virulence potential of these strains due to the broad diversity and high frequency of prophages and virulence factors found. Phylogenetic analyses were able to correctly distinguish these closely related species and show the presence of different genetic subgroups. These data contributed for a better understanding of YF, YI and YK virulence-associated features and global genetic diversity, and reinforced the need for better characterization of these Y. enterocolitica-like species considered non-pathogenic.