Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health.

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.

Flavobacterium dauae sp. nov., isolated from rhizosphere soil of a tomato plant.

A bacterial strain, designated TCH3-2T, was isolated from the rhizosphere of tomato plant grown at Dong-A University Agricultural Experiment Station, Republic of Korea. The strain was Gram-stain-negative, obligate aerobic, orange yellow-coloured, motile by gliding and short rod-shaped. Strain TCH3-2 T only grew on 1/2 tryptic soy agar and Luria-Bertani agar among the media tested, with optimum growth at 28 °C and pH 7. Salt of 1 % NaCl was necessary to support the growth of TCH3-2T. Strain TCH3-2T produced flexirubin-type pigments. The predominant cellular fatty acids were iso-C15 : 0 (55.6 %), iso-C17 : 0 3-OH (17.9 %), summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1 ω9c; 10.5 %), iso-C15 : 0 3-OH (4.8 %) and anteiso-C15 : 0 (2.3 %). The major menaquinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, five unknown aminolipids and three unknown lipids. Phylogenetic analysis based on 16S rRNA sequences indicated that TCH3-2T was closely related to Flavobacterium ummariense DS-12T (95.16 %), Flavobacterium marinum SW105T (95.14 %) and Flavobacterium viscosus YIM 102796T (94.54 %). The draft genome of TCH3-2T comprised ca. 2.8 Mb with a G+C content of 34.61 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between TCH3-2T and closely related Flavobacterium species showed that it belongs to a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of TCH3-2T from its closest relatives. Thus, chemotaxonomic characteristics together with phylogenetic affiliation illustrate that TCH3-2T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium dauae sp. nov. (type strain TCH3-2T=KACC 19054T=JCM 34025T) is proposed.

Genome Analysis of Erwinia amylovora Strains Responsible for a Fire Blight Outbreak in Korea.

Erwinia amylovora is a plant-pathogenic bacterium that causes fire blight disease in Rosaceae plants. Since fire blight is highly contagious and results in serious losses once introduced, it is regulated as a quarantine disease. Recently, for the first time in East Asia, fire blight emerged in Korea with strains of E. amylovora being isolated from lesions of infected trees. Five of those strains were selected and subjected to whole-genome shotgun sequencing. Each strain had two circular replicons, a 3.8-Mb chromosome and a 28-kb plasmid. The genome sequences were compared with those of other E. amylovora strains isolated from different hosts or geographical regions. Genome synteny was analyzed and sequence variations including nucleotide substitutions, inversions, insertions, and deletions were detected. Analysis of the population genomic structure revealed that the five strains form a distinct structural group. Phylogenomic analysis was performed to infer the evolutionary relationships among E. amylovora strains, which indicated that the Korean isolates, all descended from a common ancestor, are closely related to a lineage of North American strains. These results provide useful information for understanding the genomic dynamics of E. amylovora strains including those in Korea, developing genetic markers for surveillance of the pathogen or diagnosis of the disease, and eventually developing measures to eradicate it.

Rhizosphere microbiome structure alters to enable wilt resistance in tomato.

Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant. We cultivated this flavobacterium, named TRM1, and found that it could suppress R. solanacearum-disease development in a susceptible plant in pot experiments. Our findings reveal a role for native microbiota in protecting plants from microbial pathogens, and our approach charts a path toward the development of probiotics to ameliorate plant diseases.

Development of a risk prediction model of carbapenem-resistant Enterobacteriaceae colonization among patients in intensive care units.

BACKGROUND: Few hospitals have conducted surveillance cultures to identity carbapenem-resistant Enterobacteriaceae (CRE) colonization in Korea because of high test costs, long wait time to get results, and lack of personnel. This study aimed to identify risk factors of CRE colonization and to develop a model for predicting the risk of CRE colonization. METHODS: This retrospective cohort study was done with medical record review at a tertiary hospital between October 1, 2016, and October 31, 2017, in 444 adult patients admitted to the intensive care unit. The identification of risk factors and risk model development were done by multiple logistic regression. The area under the receiver operator characteristic curve and correct classification were measured. RESULTS: The risk prediction logistic model for CRE colonization was composed of 4 factors among 22 significant variables on univariate analysis and 1 interaction term; E (logit of CRE colonization) = -2.821 + 1.606 (isolation of multidrug-resistant organisms) + 1.347 (≥15 days of cephalosporin administration) + 0.980 (≥15 days of carbapenem administration) + 0.544 (score ≥21 on Acute Physiology and Chronic Health Evaluation II). The risk prediction model showed 0.80 (95% confidence interval, 0.74-0.85) for the area under the curve, and 68.9% correct classification. CONCLUSIONS: It is recommended to utilize the risk prediction model to screen out for the colonization of CRE, and to do validation studies for verifying the generalizability.

Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5.

Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes. Comparison of average nucleotide identities among six available Polaribacteria genomes including DSW-5 suggested that the DSW-5 genome is most similar to that of Polaribacter sp. MED152, which is a proteorhodopsin-containing marine bacterium. A phylogenomic analysis of the six Polaribacter strains and 245 Flavobacteriaceae bacteria confirmed a close relationship of the genus Polaribacter with Tenacibaculum and Kordia. DSW-5's genome has a gene encoding proteorhodopsin and genes encoding 85 enzymes belonging to carbohydrate-active enzyme families and involved in polysaccharide degradation, which may play important roles in energy metabolism of the bacterium in the marine ecosystem. With genes for 238 CAZymes and 203 peptidases, DSW-5 has a relatively high number of degrading enzymes for its genome size suggesting its characteristics as a free-living marine heterotroph.

Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).

Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of Korea, is a member of the family Erythrobacteraceae In this study, the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000 platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes were predicted.

Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function.

Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny.

Micropropagation, Acclimatization, and Greenhouse Culture of Veratrum californicum.

Micropropagation and production of Veratrum californicum is most successful when using a premixed Murishage and Skoog basal medium with vitamins and a 5-week subculture cycle at 16 °C for multiplication. These culture conditions provide the best percent survival after acclimatization in the greenhouse. However, clone response to temperature and light quality within culture conditions varies. Micropropagated plants have mass and morphology similar to 2- or 3-year-old seedlings. Acclimatized plantlets can then be grown in the greenhouse using sub-irrigation (ebb and flood) to maintain substrate volumetric water content > 44 %. Growth cycle in the greenhouse must be about 100 days, followed by dormancy for 5 months at 5 °C.

Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites.

Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds.

Effect of central line bundle on central line-associated bloodstream infections in intensive care units.

BACKGROUND: This study was conducted in 4 intensive care units (ICUs) to investigate the effect of the central line (CL) bundle on central line-associated bloodstream infection (CLABSI). METHODS: During phase 1 (baseline, from April 2009 to March 2010), active surveillance and training on hand hygiene only were conducted. During phase 2 (intervention, from April 2010 to December 2011), systemic training on the CL bundle and active surveillance and feedback with an electronic CL insertion checklist were performed. RESULTS: Adherence to the CL bundle significantly increased from 0.0% in phase 1 to 37.1% in phase 2 (P < .001), but the change of CLABSI rate was insignificant for adults in ICUs. However, adherence to the CL bundle significantly increased from 0.8% in phase 1 to 20.1% in phase 2 (P < .001), and the CLABSI rate significantly decreased from 3.7 to 0.0 per 1,000 catheter-days (P = .014) for children in ICUs. CONCLUSION: The higher adherence to the CL bundle was not positively correlated to a reduction in the CLABSI rate in adults, but it was related to a zero CLABSI for 18 months among children in the ICUs.

Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.

Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488-494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.

Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. strain G7.

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555.

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).

Draft genome sequence of the antifungal-producing plant-benefiting bacterium Burkholderia pyrrocinia CH-67.

Burkholderia pyrrocinia CH-67 was isolated from forest soil as a biocontrol agent to be utilized in agriculture. Here, we report the 8.05-Mb draft genome sequence of this bacterium. Its genome contains genes involved in biosynthesis of secondary metabolites and plant growth promotion, which may contribute to probiotic effects on plants.

Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4.

Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.

Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006.

Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.

Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches.

In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequencehomologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.

Genome sequence of the hemolytic-uremic syndrome-causing strain Escherichia coli NCCP15647.

Enterohemorrhagic Escherichia coli (EHEC) causes a disease involving diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome (HUS). Here we present the draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its genome exhibits features of EHEC, such as genes for verotoxins, a type III secretion system, and prophages.