Flavobacterium nackdongense sp. nov., a cellulose-degrading bacterium isolated from sediment.

A Gram-negative, non-motile, rod-shaped bacterial strain, designated GS13T, was isolated from sediments in a branch of the Nackdong River in Sangju, Korea. Optimal growth occurred at pH 7.0, 20 °C, and 0% NaCl. Phylogenetic analyses using 16S rRNA showed that strain GS13T is a member of the genus Flavobacterium, with highest similarity to Flavobacterium soyangense IMCC26223T (97.0%). The DNA G+C content of strain GS13T was 36.2 mol%. The dominant fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids, and one unidentified aminophospholipid. The predominant respiratory quinone was MK-6. Our data demonstrate that strain GS13T can be distinguished from closely-related Flavobacterium species. Thus, strain GS13T is a novel Flavobacterium species, and we propose the name Flavobacterium nackdongense sp. nov. The type strain is GS13T (=KCTC 62569T = JCM 32765T).

Chryseobacterium salivictor sp. nov., a plant-growth-promoting bacterium isolated from freshwater.

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated NBC 122T, was isolated from freshwater of the Nakdong River Republic of Korea. Growth occurred at pH 5.0-8.0 (optimum, pH 7.0), at 4-37 °C (optimum, 25 °C), and with 0-3.5% (w/v) NaCl (optimum, 1%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NBC 122T belongs to the genus Chryseobacterium and is most closely related to Chryseobacterium antarcticum AT1013T (97.85%). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values between strain NBC 122T and related Chryseobacterium species were 77.77-80.28 and 20.9-23.2%, respectively. The strain NBC 122T contained MK-6 as the major respiratory quinone. The major fatty acids included anteiso C15:0, iso C15:0, summed feature 9 (C17:1 iso ω9c, C16:0 10-methyl) and iso C17:0 3-OH, and the polar lipids were phosphatidylethanolamine, five unidentified aminolipids and six unidentified lipids. The DNA G + C content was 37.5 mol%. On the basis of a 16S rRNA gene phylogeny and comparative phenotypic analyses, strain NBC 122T represents a novel species in the genus Chryseobacterium, for which the name Chryseobacterium salivictor sp. nov. is proposed. The type strain is NBC122T (= KCTC 72248T = JCM 33980T).

Ephemeroptericola cinctiostellae gen. nov., sp. nov., isolated from gut of an aquatic insect.

A Gram-stain-negative, catalase- and oxidase-positive, non-motile bacterium, designated F02T, was isolated from of gut of Cincticostellalevanidovae (Tshernova). Growth occurred at a temperature range of 4-30 °C, at pH 6-9 and in the presence of 0-0.5 % (w/v) NaCl. Phylogenetic analysis demonstrated that the 16S rRNA gene sequence of strain F02T shared the highest similarity to that of the type strain of Hydromonas duriensis A2P5T (96.82 %). The major isoprenoid quinone was Q-8. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C13 : 0 3-OH. The polyamines were cadaverine and putrescine. Combined data from phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain F02T represents a novel genus and species, for which the name Ephemeroptericolacinctiostellae gen. nov., sp. nov. is proposed. The type strain of Ephemeroptericola cinctiostellae gen. nov., sp. nov. is F02T (=FBCC 500047T=KCTC 62567T=JCM 32722T).

Flavobacterium sangjuense sp. nov. isolated from sediment.

A yellow-pigmented bacterial strain, GS03T, was isolated from sediment in a branch of the Nackdong River in Sangju, Korea. Cells were observed to be Gram-negative, aerobic and rod-shaped with gliding motility, and to be positive for catalase and oxidase. Growth was found to occur at 4-30 °C (optimum 25 °C), at pH 7.0-8.5 (optimum pH 7.5) and at NaCl 0% (optimum NaCl 0%, w/v). The major cellular fatty acids (> 10% of the total) were identified as iso C15:0, iso C15:1 G, C15:1ω6c, iso C15: 0 3-OH and iso C17: 0 3-OH. The major respiratory quinone was found to be menaquinone MK-6. The genome sequence of GS03T is 3.1 Mb with G+C content of 36.1 mol%. The major polar lipids of the isolate were identified as phosphatidylethanolamine, three unidentified aminolipids, two unidentified phospholipids, an unidentified lipid and an unidentified aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GS03T clusters with Flavobacterium paronense KNUS1TT, with similarity of 96.8%. The phenotypic, phylogenetic, and chemotaxonomic characteristics indicate that strain GS03T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium sangjuense sp. nov. is proposed. The type strain is GS03T (= FBCC 502459T = KCTC 62568T = JCM 32764T).

Genes involved in nutrient competition by Pseudomonas putida JBC17 to suppress green mold in postharvest satsuma mandarin.

Understanding the mechanisms underlying biocontrol activity in biocontrol agents is indispensable to implement biological control. However, the understanding of specific mechanisms for nutrient competition in nutrient limited environments is still limited. This study was performed to control green mold of postharvest satsuma mandarin (mandarin) using Pseudomonas putida JBC17 (JBC17), and identify the genes involved in nutrient competition. Treatment with JBC17 on wounded mandarin fruits at a concentration of 10(6) and 10(7) cfu ml(-1) suppressed the incidence of green mold with efficacy of 74.1 and 91.4%, respectively, compared to the untreated control. In spite of there being no antifungal activity in a dual culture test, JBC17 significantly inhibited the conidial germination of Penicillium digitatum. The results from the nutrient competition assay revealed that the inhibition of conidial germination was exerted by nutrient starvation. From the constructed transposon (Tn) library of JBC17, exopolyphosphatase (ppx) and Xaa-Pro aminopeptidase (pepP) were recognized as potential factors responsible for the inhibition of conidial germination. In conclusion, the understanding of nutrient depletion specific to the inhibition of conidial germination by JBC17 may ultimately lead to a deeper understanding of the bacterial metabolism and conidial metabolism for germination as well as biocontrol activity.

Protective Effect of Anthocyanin-Enriched Polyphenols from Hibiscus syriacus L. (Malvaceae) against Ultraviolet B-Induced Damage.

Anthocyanin-enriched polyphenols from the flower petals of H. syriacus L. (Malvaceae, AHs) possess anti-septic shock, anti-oxidant, and anti-melanogenic properties. However, whether AHs positively or negatively regulate ultraviolet B (UVB)-mediated photoaging and photodamage remains unclear. This study aims to investigate the protective effect of AHs against UVB-induced damage. We examined the photoprotective effects of AHs on UVB-induced apoptosis, endoplasmic reticulum (ER) stress, and mitochondrial reactive oxygen species (mtROS). AHs prevented UVB irradiation-induced apoptosis of HaCaT keratinocytes by inhibiting caspase activation and ROS production. Moreover, AHs restored the survival rate and the hatchability of UVB-irradiated zebrafish larvae without any abnormalities. Furthermore, AHs inhibited UVB-induced ER stress, resulting in a decrease in mtROS production via the stabilization of the mitochondrial membrane potential. Our results indicate that AHs inhibit UVB-induced apoptosis by downregulating total cytosolic ROof cytosolic CaS and ER-mediated mitoROS production in both HaCaT keratinocytes and zebrafish larvae. These findings provide evidence for the applications of AHs to protect skin from UVB-induced photodamage.

Complete Genome Sequence of Chryseobacterium sp. Strain NBC 122, a Plant Growth-Promoting Bacterium Isolated from Freshwater.

Chryseobacterium sp. strain NBC 122, isolated from freshwater of the Nakdong River in the Republic of Korea, was previously characterized as a plant growth-promoting bacterium. Here, we report the genome sequence of Chryseobacterium sp. NBC 122.

Assessment of the Contribution of Antagonistic Secondary Metabolites to the Antifungal and Biocontrol Activities of Pseudomonas fluorescens NBC275.

An understanding of the contribution of secondary metabolites (SMs) to the antagonistic and biocontrol activities of bacterial biocontrol agents serves to improve biocontrol potential of the strain. In this study, to evaluate the contribution of each SM produced by Pseudomonas fluorescens NBC275 (Pf275) to its antifungal and biocontrol activity, we combined in silico analysis of the genome with our previous study of transposon (Tn) mutants. Thirteen Tn mutants, which belonged to 6 biosynthetic gene clusters (BGCs) of a total 14 BGCs predicted by the antiSMASH tool were identified by the reduction of antifungal activity. The biocontrol performance of Pf275 was significantly dependent on 2,4-diacetylphloroglucinol and pyoverdine. The clusters that encode for arylpolyene and an unidentified small linear lipopeptide influenced antifungal and biocontrol activities. To our knowledge, our study identified the contribution of SMs, such as a small linear lipopeptide and arylpolyene, to biocontrol efficacy for the first time.

Control of Anthracnose and Gray Mold in Pepper Plants Using Culture Extract of White-Rot Fungus and Active Compound Schizostatin.

Fungi produce various secondary metabolites that have beneficial and harmful effects on other organisms. Those bioactive metabolites have been explored as potential medicinal and antimicrobial resources. However, the activities of the culture filtrate (CF) and metabolites of white-rot fungus (Schizophyllum commune) have been underexplored. In this study, we assayed the antimicrobial activities of CF obtained from white-rot fungus against various plant pathogens and evaluated its efficacy for controlling anthracnose and gray mold in pepper plants. The CF inhibited the mycelial growth of various fungal plant pathogens, but not of bacterial pathogens. Diluted concentrations of CF significantly suppressed the severity of anthracnose and gray mold in pepper fruits. Furthermore, the incidence of anthracnose in field conditions was reduced by treatment with a 12.5% dilution of CF. The active compound responsible for the antifungal and disease control activity was identified and verified as schizostatin. Our results indicate that the CF of white-rot fungus can be used as an eco-friendly natural product against fungal plant pathogens. Moreover, the compound, schizostatin could be used as a biochemical resource or precursor for development as a pesticide. To the best of our knowledge, this is the first report on the control of plant diseases using CF and active compound from white-rot fungus. We discussed the controversial antagonistic activity of schizostatin and believe that the CF of white-rot fungus or its active compound, schizostatin, could be used as a biochemical pesticide against fungal diseases such as anthracnose and gray mold in many vegetables.

Comparison of the Genetic Alterations between Primary Colorectal Cancers and Their Corresponding Patient-Derived Xenograft Tissues.

Patient-derived xenograft (PDX) models are useful tools for tumor biology research and testing the efficacy of candidate anticancer drugs targeting the druggable mutations identified in tumor tissue. However, it is still unknown how much of the genetic alterations identified in primary tumors are consistently detected in tumor tissues in the PDX model. In this study, we analyzed the genetic alterations of three primary colorectal cancers (CRCs) and matched xenograft tissues in PDX models using a next-generation sequencing cancer panel. Of the 17 somatic mutations identified from the three CRCs, 14 (82.4%) were consistently identified in both primary and xenograft tumors. The other three mutations identified in the primary tumor were not detected in the xenograft tumor tissue. There was no newly identified mutation in the xenograft tumor tissues. In addition to the somatic mutations, the copy number alteration profiles were also largely consistent between the primary tumor and xenograft tissue. All of these data suggest that the PDX tumor model preserves the majority of the key mutations detected in the primary tumor site. This study provides evidence that the PDX model is useful for testing targeted therapies in the clinical field and research on precision medicine.

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202.

Maintenance of a beneficial microbial community, especially in the rhizosphere, is indispensable for plant growth and agricultural sustainability. In this sense, plant growth-promoting rhizobacteria (PGPR) have been extensively studied for their role in plant growth promotion and disease resistance. However, the impact of introducing PGPR strains into rhizosphere microbial communities is still underexplored. We previously found that the Proteus vulgaris JBLS202 strain (JBLS202) promoted growth of Kimchi cabbage and altered the relative abundance of total bacteria and Pseudomonas spp. in the treated rhizosphere. To extend these findings, we used pyrosequencing to analyze the changes in bacterial communities in the rhizosphere of Kimchi cabbage after introduction of JBLS202. The alterations were also evaluated by taxon-specific real-time PCR (qPCR). The pyrosequencing data revealed an increase in total bacteria abundance, including specific groups such as Proteobacteria, Acidobacteria, and Actinobacteria, in the treated rhizosphere. Time-course qPCR analysis confirmed the increase in the abundance of Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. Furthermore, genes involved in nitrogen cycling were upregulated by JBLS202 treatment indicating changes in ecological function of the rhizosphere soil. Overall, these results indicate that introduction of JBLS202 alters both the composition and function of the rhizosphere bacterial community, which can have direct and indirect effects on plant growth. Therefore, we propose that long-term changes in bacterial composition and community-level function need to be considered for practical use of PGPRs.

Effects of flaC Mutation on Stringent Response-Mediated Bacterial Growth, Toxin Production, and Motility in Vibrio cholerae.

The stringent response (SR), which is activated by accumulation of (p)ppGpp under conditions of growth-inhibiting stresses, plays an important role on growth and virulence in Vibrio cholerae. Herein, we carried out a genome-wide screen using transposon random mutagenesis to identify genes controlled by SR in a (p)ppGpp-overproducing mutant strain. One of the identified SR target genes was flaC encoding flagellin. Genetic studies using flaC and SR mutants demonstrated that FlaC was involved in bacterial growth, toxin production, and normal flagellum function under conditions of high (p)ppGpp levels, suggesting FlaC plays an important role in SR-induced pathogenicity in V. cholerae.

Diversity of bacteriophages infecting Xanthomonas oryzae pv. oryzae in paddy fields and its potential to control bacterial leaf blight of rice.

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a very serious disease in rice-growing regions of the world. In spite of their economic importance, there are no effective ways of protecting rice plants from this disease. Bacteriophages infecting Xoo affect the population dynamics of the pathogen and consequently the occurrence of the disease. In this study, we investigated the diversity, host range, and infectivity of Xoo phages, and their use as a bicontrol agent on BLB was tested. Among the 34 phages that were isolated from floodwater in paddy fields, 29 belonged to the Myoviridae family, which suggests that the dominant phage in the ecosystem was Myoviridae. The isolated phages were classified into two groups based on plaque size produced on the lawn of Xoo. In general, there was a negative relationship between plaque size and host range, and interestingly the phages having a narrow host range had low efficiency of infectivity. The deduced protein sequence analysis of htf genes indicated that the gene was not a determinant of host specificity. Although the difference in host range and infectivity depending on morphotype needs to be addressed, the results revealed deeper understanding of the interaction between the phages and Xoo strains in floodwater and damp soil environments. The phage mixtures reduced the occurrence of BLB when they were treated with skim milk. The results indicate that the Xoo phages could be used as an alternative control method to increase the control efficacy and reduce the use of agrochemicals.