An ethanol-utilizing Fe(III)-reducing bacterial strain, OSK2AT, was isolated from a lotus field in Aichi, Japan. Phylogenetic analysis of the 16S rRNA gene sequences of OSK2AT and related strains placed it within Geobacter sulfurreducens PCAT. Strain OSK2AT was shown to be a Gram-negative, motile, rod-shaped bacterium, strictly anaerobic, 0.76−1.65 µm long and 0.28−0.45 μm wide. Its growth occurred at 20−40℃, pH 6.0−8.1, and it tolerated up to 1% NaCl. The G+C content of the genomic DNA was 61.2 mol% and DNA-DNA hybridization value with Geobacter sulfurreducens PCAT was 60.7%. The major respiratory quinone was MK-8. The major fatty acids were 16：1 ω7c, 16：0, 14：0, 15：0 iso, 16：1 ω5c, and 18：1 ω7c. Strain OSK2AT could utilize H2, ethanol, acetate, lactate, pyruvate, and formate as substrates with Fe(III)-citrate as electron acceptor. Amorphous Fe(III) hydroxide, Fe(III)-NTA, fumarate, malate, and elemental sulfur were utilized as electron acceptors with either acetate or ethanol as substrates. Results obtained from physiological, DNA-DNA hybridization, and chemotaxonomic tests support genotypic and phenotypic differentiation of strain OSK2AT from its closest relative. The isolate is assigned as a novel subspecies with the name Geobacter sulfurreducens subsp. ethanolicus, subsp. nov. (type strain OSK2AT=DSMZ 26126T=JCM 18752T).
The present study determined the complete rpoB and seven partial house-keeping gene sequences of 29 human (20) and poultry (9) strains of Staphylococcus aureus, and conducted a phylogenetic analysis together with 39 strains in the GenBank and EMBL databases. On the basis of complete rpoB gene sequence (RS) typing , 28 different rpoB sequence types (RSTs) were identified; however, only 23 multilocus sequence types (STs) were identified by multi-locus sequence typing (MLST). RST 2-1 was a major RST covering 23.5% (16/68) of the analyzed strains followed by RST 4-1 (14.7%, 10/68). Out of 10 poultry strains including one in the database, 9 and 1 were classified into unique RSTs 3-1 and 6-3, respectively. According to the MLST, ST5 was a major sequence type covering 25.0% (17/68) of them, followed by STs 228 and 239 (for each ST, 11.8%, 8/68), and poultry strains were grouped into ST5 (9/10) and ST692 (1/10). The poultry ST5 strains were differentiated from human ST5 strains and rifampin resistance-related mutations were observed in some human S. aureus strains by RS typing. Thus, RS typing was more discriminative and informative than MLST, and it can be a simple and economic alternative to MLST for identification and phylogenetic analysis of S. aureus.
A Gram-staining-negative, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium designated THG 07T was isolated from the soil of a ginseng field of Pocheon in South Korea, and its taxonomic position was investigated by using a polyphasic study. Strain THG 07T grew optimally at 25−30°C and at pH 6.5−7.0 and in the absence of NaCl on nutrient agar. Strain THG-T17T displayed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant ginsenosides of ginseng) to compound C-K. On the basis of 16S rRNA gene sequence similarity, strain THG 07T was shown to belong to the family Sphingobacteriaceae and was related to Sphingobacterium canadense CR11T (98.7%), S. cladoniae No.6T (98.1%), S. detergens 6.2ST (98.0%), S. multivorum IAM14316T (97.9%), S. siyangense SY1T (97.8%) and S. thalpophilum DSM11723T (96.9%). The G+C content of the genomic DNA was 40.6 mol%. The major menaquinone, MK-7, and major fatty acids, iso-C15:0 and C16:1 ω7c and/or ω6c, supported the affiliation of strain THG 07T to the genus Sphingobacterium. The DNA-DNA relatedness values between strain THG 07T and its closest phylogenetic neighbors were below 26.9%. The results of physiological and biochemical tests enabled strain THG 07T to be differentiated phenotypically from the recognized species of the genus Sphingobacterium. Therefore the isolate represents a novel species, for which the name Sphingobacterium ginsenosidimutans sp. nov. is proposed, with the type strain THG 07T (=KACC 14526T=JCM 16722T).
To better understand the phosphorus (P) cycling in an agricultural soil environment, amounts of total, organic and inorganic P in 10 agricultural soil samples were analyzed. Since a large proportion (57.8%) of the total P in the soils was in organic form, a method was developed to evaluate the mineralization rate of organic P in the soil by adding phytate to the soil and analyzing the change in water-soluble P (WSP) content after incubating it for 3 days. Moreover, the relationship between the phytate mineralization activity and bacterial biomass in 60 agricultural soils was also investigated, where the phytate mineralization activity ranged from 0 to 61.7% (average: 18.8%), and the R2 value between phytate mineralization activity and indigenous bacterial biomass was 0.11 only. Phytate-degrading bacteria were isolated from the soil environment, and identified as Pseudomonas rhodesiae JT29, JT32, JT33, JT34, JT35, Pseudomonas sp. JT30, and Flavobacterium johnsoniae JT31. When P. rhodesiae JT29 and F. johnsoniae JT31 were inoculated into the agricultural soils, the phytate mineralization activities were increased up to 16 and 27 times, respectively. It was concluded that promotion of effective phytate-degrading bacterial strains could improve the sustainable P management in the agricultural soils.
Complete genome sequencing of Naegleria gruberi has revealed that the organism encodes polypeptides similar to photoactivated adenylyl cyclases (PACs). Screening in the N. australiensis genome showed that the organism also encodes polypeptides similar to PACs. Each of the Naegleria proteins consists of a “sensors of blue-light using FAD” domain (BLUF domain) and an adenylyl cyclase domain (AC domain). PAC activity of the Naegleria proteins was assayed by comparing sensitivities of Escherichia coli cells heterologously expressing the proteins to antibiotics in a dark condition and a blue light-irradiated condition. Antibiotics used in the assays were fosfomycin and fosmidomycin. E. coli cells expressing the Naegleria proteins showed increased fosfomycin sensitivity and fosmidomycin sensitivity when incubated under blue light, indicating that the proteins functioned as PACs in the bacterial cells. Analysis of the N. fowleri genome revealed that the organism encodes a protein bearing an amino acid sequence similar to that of BLUF. A plasmid expressing a chimeric protein consisting of the BLUF-like sequence found in N. fowleri and the adenylyl cyclase domain of N. gruberi PAC was constructed to determine whether the BLUF-like sequence functioned as a sensor of blue light. E. coli cells expressing a chimeric protein showed increased fosfomycin sensitivity and fosmidomycin sensitivity when incubated under blue light. These experimental results indicated that the sequence similar to the BLUF domain found in N. fowleri functioned as a sensor of blue light.