A Gram-negative, rod-shaped, non-spore-forming and motile bacterial strain TR7-01T was isolated from a compost soil in South Korea and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TR7-01T belonged to the genus Hydrogenophaga within the class Betaproteobacteria. Strain TR7-01T exhibited 16S rRNA gene sequence similarity values of 95.0−98.3% to members of the genus Hydrogenophaga: Hydrogenophaga bisanensis DSM12412T (98.3%), Hydrogenophaga flava DSM 619T (97.1%), Hydrogenophaga pseudoflava ATCC 33668T (96.8%), Hydrogenophaga intermedia S1T (96.4%), Hydrogenophaga atypica BSB 41.8T (95.8%), Hydrogenophaga defluvii BSB 9.5T (95.7%), Hydrogenophaga palleronii CCUG 20334T (95.6%), Hydrogenophaga caeni EMB71T (95.4%) and Hydrogenophaga taeniospiralis ATCC 49743T (95.0%). Chemotaxonomic data revealed that strain TR7-01T possesses ubiquinone Q-8, the G+C content was 69.9 mol%, and the predominant fatty acids were 16 : 1 ω7c/15 : 0 iso 2OH, 18 : 1 ω7c/ω9t/ω12t and C16:0, all of which corroborated our assignment of the strain to the genus Hydrogenophaga. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that strain TR7-01T represents a distinct species. Based on these data, TR7-01T (= KCTC 12203T = DSM 18117T) should be classified as a novel Hydrogenophaga species, for which the name Hydrogenophaga temperata sp. nov. has been proposed.
Two Gram-positive bacteria, designated strains Aji5-31T and Ngc37-23T, were isolated from the intestinal tracts of fishes. 16S rRNA gene sequence analysis indicated that both strains were related to the members of the family Dermatophilaceae, with 95.6-96.9% 16S rRNA gene sequence similarities. The family Dermatophilaceae contains 2 genera and 3 species: Dermatophilus congolensis, Dermatophilus chelonae and Kineosphaera limosa. However, it has been suggested that the taxonomic position of D. chelonae should be reinvestigated using a polyphasic approach, because the chemotaxonomic characteristics are not known (Stackebrandt, 2006; Stackebrandt and Schumann, 2000). Our present study revealed that strains Aji5-31T, Ngc37-23T and D. chelonae NBRC 105200T should be separated from the other members of the family Dermatophilaceae on the basis of the following characteristics: the predominant menaquinone of strain Aji5-31T is MK-8(H2), strain Ngc37-23T possesses iso- branched fatty acids as major components, and the menaquinone composition of D. chelonae is MK-8(H4), MK-8 and MK-8(H2) (5 : 3 : 2, respectively). On the basis of these distinctive phenotypic characteristics and phylogenetic analysis results, it is proposed that strains Aji5-31T and Ngc37-23T be classified as two novel genera and species of the family Dermatophilaceae. The names are Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., and the type strains are Aji5-31T (=NBRC 104925T =DSM 22762T) and Ngc37-23T (=NBRC 104926T =DSM 22761T), respectively. In addition, D. chelonae should be reassigned to a new genus of the family Dermatophilaceae with the name Austwickia chelonae gen. nov., comb. nov.
The rice blast fungus Magnaporthe oryzae produces appressoria during the infection of a host. In M. oryzae, the appressorium formation-related gene CBP1 (Chitin Binding Protein 1) is specifically expressed during the early stage of appressorium differentiation. The transcription factor CON7 activates CBP1 expression. However, many aspects of the regulation of CBP1 expression are still unknown. In this report, the CBP1 5′ upstream region was analyzed using an egfp reporter. Deletion of the CBP1 5 ′ upstream region caused derepression of reporter gene activity during vegetative growth. This result suggests that CBP1 expression is repressed during vegetative growth. The key 5 ′ upstream sequences for CBP1 repression were examined. Furthermore, cis- and trans-acting elements of the negative regulatory region were investigated. Here, we discuss the transcriptional regulatory mechanism of CBP1.
In the course of a study on yeast diversity in Japan, we isolated 331 yeast strains from natural substrates in Rishiri Island, which belongs to the subarctic zone. Among the isolates from soil, two strains produced hat-shaped ascorspores and showed that reproduction occurred by conjugation of a larger cell and a smaller one. We surveyed strains preserved in our culture collection, NBRC, and found one Barnettozyma strain; thus we examined these three strains. A phylogenetic tree based on the D1/D2 domain of 26S rDNA (D1/D2) shows that these strains are included in the Barnettozyma clade, but clearly separated from the known Barnettozyma and Candida species within the clade. This group is distinguishable from B. vustinii by the ability to assimilate sucrose and maltose, and from B. populi by the ability to ferment glucose and to assimilate L-sorbose, sucrose, maltose, α-methyl-D-glucoside, and salicin. We propose that the group represent a new species, B. sucrosica sp. nov. (NBRC 105021T=CBS 11512T, Mycobank no. MB515733).
To elucidate the role of Abf2p, a major mitochondrial DNA-binding protein in the yeast Saccharomyces cerevisiae, we examined the morphology of the mitochondrial nucleoids (mt-nucleoids) in an ABF2-deficient mutant (Δabf2) in vivo and in vitro by 4′,6-diamidino-2-phenylindole (DAPI) staining. The mt-nucleoids appeared as diffuse structures with irregular-size in Δabf2 cells that were grown to log phase in YPG medium containing glycerol, in contrast to the strings-of-beads appearance of mt-nucleoids in wild-type cells. In addition, DAPI-fluorescence intensity of the mt-nucleoids transmitted to the bud was significantly lower in Δabf2 cells than in wild-type cells at log phase. However, the lack of Abf2p did not affect the morphology or segregation of mitochondria. The protein composition of the mt-nucleoids isolated from Δabf2 cells grown to stationary phase in YPG medium was very similar to that of the mt-nucleoids isolated from wild-type cells cultured under the same conditions, except for the lack of Abf2p. These results together suggested that in log-phase cells, the lack of Abf2p influences not only the morphology of mt-nucleoids but also their transmission into the bud. On the other hand, our result suggested that in stationary-phase cells, the lack of Abf2p does not significantly alter the protein composition of the mt-nucleoids.
A selective enrichment broth (SVV) was formulated to allow concurrent growth of Salmonella spp., V. parahaemolyticus, and V. cholerae. Potassium tellurite and sodium citrate were added as the inhibitors, while glucose, mannitol, anhydrous sodium sulfite and sodium pyruvate were employed as the growth-promoters. When mixed in equal or varied proportions, the target pathogens in SVV had a great accumulation (105-108 CFU/ml) and effectively inhibited the growth of competitive microflora. In the artificially contaminated samples, a high recovery of these 3 target pathogens was obtained in SVV. Finally, Salmonella spp., V. parahaemolyticus, and V. cholerae were detected from 608 suspicious food samples by SVV with real-time PCR, and no false-positive or -negative results were reported. In summary, SVV has been shown to be a suitable broth for the simultaneous detection of the 3 pathogens by multipathogen detection on a single-assay platform.
Three Gram-negative, motile, coccoid- and ellipsoidal-shaped, non-pigmented, chemoheterotrophic bacteria, designated strains SA4-31, SA4-46 and SA4-48T, were isolated from Lake Saroma in Japan and subjected to a polyphasic taxonomical study. 16S rRNA gene sequence analysis revealed that the novel isolates could be affiliated to the family Pseudoalteromonadaceae of the order Alteromonadales. The strains shared approximately 99.7-100% sequence similarity with each other and showed 89.5-93.2% similarity with members of the family Pseudoalteromonadaceae with validly published names. The DNA-DNA relatedness among the strains SA 4-31, SA 4-46 and SA 4-48T was higher than 80%, a value that is accepted as a phylogenetic definition of one species. The DNA G+C contents of the three strains were 38.7-39.6 mol%. The major isoprenoid quinone was Q-8 and C16:0, C16:1 ω7c, C18:1 ω7c and C12:1 3OH were the major fatty acids. Based on the evidence from the polyphasic taxonomical study, it was concluded that the three strains should be classified as representing a new genus and species of the family Pseudoalteromonadaceae, for which the name Psychrosphaera saromensis gen. nov., sp. nov. (type strain SA4-48T =NBRC 107123T= KCTC 23240T) is proposed.
TKU010 was isolated from infant vomited milk and identified as Lactobacillus paracasei subsp. paracasei. TKU010 had desirable properties concerning its ability to withstand adverse conditions in the gastrointestinal tract. The hydrolysate of casein enhanced the growth of TKU010 most obviously (17.20-18.25 OD660), followed by the hydrolysate of SPP (16.00-15.06 OD660). Incubating with SPP, both the culture supernatant of TKU010 on the first day and the fourth day showed inhibitory activities on E. coli BCRC13086, F. oxysporum BCRC32121 and A. fumigatus BCRC30099. TKU010 culture supernatant (1% SPP) incubated for 3 days has high antioxidant activity; the DPPH scavenging ability was 75% per ml. Thus, TKU010 could be preferably used as a starter to produce fermented milk with possibly interesting organoleptic properties. Besides, we have shown that squid pen wastes can be utilized to generate a high value-added product, and have revealed its hidden potential in the production of biocontrol agents and functional foods.
Locus afe_0454 from Acidithiobacillus ferrooxidans (At.ferrooxidans) is annotated as related to copper resistance in The Institute for Genomic Research database. In our study, two At.ferrooxidans strains, 26# and DC, with different levels of copper ion resistance were isolated from acid mine drainages at two major copper mines in China, and their copper-resistance capacity was determined. The 26# strain had a copper-tolerance level of 0.22 mol/L, whereas the DC strain had a lower copper-tolerance level of 0.04 mol/L. The mutant 26# was generated from strain 26#, and its copper-tolerance level was 0.25 mol/L. Using real-time quantitative reverse transcription polymerase chain reaction, differential expression of the afe_0454 gene during copper ion stress of these three strains was investigated. The results showed that the expression of afe_0454 was increased under copper ion stress, indicating that the afe_0454 gene is sensitive to copper levels. Furthermore, the afe_0454 gene expression ratio varied in the different copper-resistant strains. Gene expression was highest in the highest copper-resistant strain. The deduced amino acid sequence of the afe_0454 gene was 56.87% non-polar, indicating the AFE_0454 protein was hydrophobic. Searching with the AFE_0454 protein in The Institute for Genomic Research database showed that the structure of the copper resistance protein D (CopD), which transports copper ions outside of the cell, had the highest sequence identity (46%). Bioinformatics analysis showed that the AFE_0454 protein has eight transmembrane helixes and was predicted to be localized to the plasma membrane. These results strongly suggested that the AFE_0454 protein is likely a transmembrane protein and might be directly involved in copper ion resistance.