Dickeya colocasiae sp. nov. isolated from wetland taro, Colocasia esculentum

Bacterial pathogens identified as Dickeya sp. have recently been associated with a corm rot of wetland taro on Oahu, Hawaii, but the species designation of these strains was unclear. A Gram-negative, pectinolytic bacterial strain PL65T isolated from an infected taro corm was subjected to polyphasic analysis to determine its genomic and phenotypic characteristics. Multi-locus sequence analyses (MLSA) based on five housekeeping genes (dnaA, gapA, gyrB, atpD, and purA) revealed that Dickeya zeae and D. oryzae, were the closest relatives. Phylogenetic analysis based on 463 core gene sequences clearly showed two potentially new species within Dickeya oryzae. In silico DNA-DNA hybridization value of strain PL65T with 12 Type strains of Dickeya species was <68%. Average nucleotide identity (ANI) analysis revealed that PL65T was at the margin of the species delineation cut-off values with a 96% ANI value. The metabolic profile of strain PL65T using BIOLOG differentiated it from the type strains of all other known species of Dickeya. Based on the results of genome-to-genome comparisons and phenotypic data presented in this report, we propose establishment of a new species, Dickeya colocasiae sp. nov. with strain PL65T as the type strain (ICMP 24361T).

Pseudomonas Tumuqiensis Sp. Nov., Isolated From Greenhouse Soil

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT was 97.4%. Phylogenetic analysis base on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that LAMW06T represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with the DNA G+C content of 63.5 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and Pseudomonas cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5 % and 43.0%, 25.9%, 24.6 % respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqiensis sp. nov. is proposed. The type strain is LAMW06T (=GDMCC 1.2003T =KCTC 72829T).

Electrochemical Detection Platform Based on RGO Functionalized with Diazonium Salt for DNA Hybridization

In this paper, we propose an improved electrochemical platform based on graphene for the detection of DNA hybridization. Commercial screen-printed carbon electrodes (SPCEs) were used for this purpose due to their ease of functionalization and miniaturization opportunities. SPCEs were modified with reduced graphene oxide (RGO), offering a suitable surface for further functionalization. Therefore, aryl-carboxyl groups were integrated onto RGO-modified electrodes by electrochemical reduction of the corresponding diazonium salt to provide enough reaction sites for the covalent immobilization of amino-modified DNA probes. Our final goal was to determine the optimum conditions needed to fabricate a simple, label-free RGO-based electrochemical platform to detect the hybridization between two complementary single-stranded DNA molecules. Each modification step in the fabrication process was monitored by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) using [Fe(CN)6]3−/4− as a redox reporter. Although, the diazonium electrografted layer displayed the expected blocking effect of the charge transfer, the next steps in the modification procedure resulted in enhanced electron transfer properties of the electrode interface. We suggest that the improvement in the charge transfer after the DNA hybridization process could be exploited as a prospective sensing feature. The morphological and structural characterization of the modified electrodes performed by scanning electron microscopy (SEM) and Raman spectroscopy, respectively, were used to validate different modification steps in the platform fabrication process.

Lelliottia Rebaudianalis Sp. Nov. Isolated From Wild Stevia Rebaudiana Bertoni

A Gram-stain-negative, aerobic, chemoheterotrophic bacterium, characterized with rod shape and mobility, designated as LST-1T, was isolated from wild Stevia rebaudiana Bertoni and subjected to polyphasic taxonomic analysis. The LST-1T strain grew optimally at 37 °C and pH 6.0–7.0 in the presence of 0.5 % (w/v) NaCl. Phylogenetic sequence analysis based on 16S rDNA from LST-1 indicated that it is close to Lelliottia jeotgali (99.85%), Lelliottia nimipressuralis (98.82%), and Lelliottia amnigena (98.54%). Multi-locus sequence typing analysis of concatenated partial recA, atpD, and infB was performed to improve resolution, and clear distinctions between the closest related type strains were exhibited. Meanwhile, the results from average nucleotide identify analyses and DNA–DNA hybridization with four species (16S rDNA similarity > 98.65%) were less than 90% and 40% respectively, verifying the distinct characteristics from other species of Lelliottia, The cellular fatty acid profile of the strain consisted of C16:0, Summed Feature3, and Summed Feature8 (may be 16:1 w6c/16:1 w7c and 18:1 w6c) as major components. The major polar lipids included phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, three non-characteristic phospholipids, and a non-characteristic lipid. The genome of LST-1T is 4,611,055 bp, with a DNA G + C content of 55.02%. Combination of several phenotypic, chemotaxonomic, and genomic characteristics proved that the LST-1T strain does represent a novel genus, for which the name Lelliottia sp. LST-1 was proposed. The type strain is LST-1T (= CGMCC 1.19175T = JCM 34938T).

Microvirga Puerhi Sp. Nov., Isolated from Puerh Tea Garden Soil

Strain WGZ8T was isolated from a soil sample of Puerh tea garden in Puer city, Southwest China. The isolate was rod-shaped, Gram-stain negative, aerobic, non-motile. Growth occurred within 0-3.0% (w/v) NaCl (optimal concentration, 0-1.0%), pH 5.0-11.0 (optimal pH, 7.0) and 10-40°C (optimal temperature, 28°C). 16S rRNA gene sequences based phylogenetic and phylogenomic analysis revealed that WGZ8T belonged to the genus Microvirga. Its major cellular fatty acids were C19:0 cyclo ω8c, C16:0, C18:1ω7c and/or C18:1ω6c. The profile of polar lipids included phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidyl-glycerol. The only respiratory quinone was detected as ubiquinone 10 (Q-10). The genome size of strain WGZ8T was 5.17MB, and the content of DNA G+C was 61%. Based on the results of digital DNA-DNA hybridization and phenotypic results, strain WGZ8T could be concluded as a novel species of the genus Microvirga, for which the name Microvirga puerhi sp. nov. is proposed. The type strain is WGZ8T (=CGMCC 1.19171T=JCM XXXXT).

Peptoniphilus Colimassiliensis sp. nov. and Peptoniphilus Urinimassiliensis sp. nov., Two New Species Isolated From Humans

Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive cocci bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37°C in anaerobic conditions. They also metabolize carbohydrates such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains, Marseille-P3761 (38%) and Marseille-P3195 (31%). The highest DNA-DNA hybridization values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that strains Marseille-P3761 (CSUR P3761 = CCUG71569) and Marseille-P3195 (CSUR P3195 = DSM 103468) are the type strains of two new Peptoniphilus species, for which we propose the names Peptoniphilus colimassiliensis sp. nov. and Peptoniphilus urinimassiliensis sp. nov., respectively.

A Lattice Model on the Rate of DNA Hybridization

We develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc) and trap-correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (kN) is directly proportional to the collision rate and the average number of correct-contacts (<ncc>) formed when both the c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈n_cc 〉∝L⁄V where L is the length of c-ssDNAs and V is the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (Rg) with their length as R_g∝√L. Since the reaction space will be approximately a sphere with radius equals to 2Rg and V∝L^(3⁄2), one obtains k_N∝1/√L. When c-ssDNAs are nonrepetitive, then the overall renaturation rate becomes as k_R∝k_N L and one finally obtains k_R∝√L in line with the experimental observations. When c-ssDNAs are repetitive with a complexity of c, then earlier models suggested the scaling k_R∝√L/c which breaks down at c = L. This clearly suggested the existence of at least two different pathways of renaturation in case of repetitive c-ssDNAs viz. via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close vicinity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, then the pathway via incorrect contacts will dominate. When the complexity is much lesser than the length of c-ssDNA, then pathway via trap correct contacts would be the dominating one.

Quantitative Performance Analysis of Flexible Ink-jet Printed Low-cost DNA Sensors Based on a CNT Network

We report the design, fabrication and quantitative performance analysis of a low-cost, flexible carbon nanotube (CNT) network-based deoxyribonucleic acid (DNA) sensor. These sensors comprise an array of ink-jet printed silver (Ag) electrodes on a transparent polyethylene terephthalate (PET) flexible substrate, where a CNT network acts as a sensing layer. The DNA hybridization is studied by immobilizing single-stranded DNA (ssDNA) probes on the CNT surface; these probes recognize their complementary DNA target. Further, we have carried out a quantitative performance analysis of the flexible CNT biosensors using the analytic hierarchy process (AHP). We have identified various influencing factors and sub-factors (performance indicators), and quantified the performance of the flexible CNT biosensors in different measured states (before bending, during bending and after bending). Additionally, the noise and other external factors contributing to the measured real signal have been quantified. The interpretation of the overall outcome will enable the improvement of the performance of flexible biosensors fabricated through large-scale manufacturing for possible commercialization.

Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens

This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum . A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum . Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum . The genome sequences of the strains had average nucleotide identity values ranging from 94.35–95.19 % and in silico DNA–DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.