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A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya , with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya . Based on the results of the polyphasic approaches, we propose that strain ZYY5T represents a novel species in the genus Dickeya , for which the name Dickeya oryzae sp. nov. (=JCM 33020 T=ACCC 61554 T) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5T.

Genetic engineering plays a unique role in fundamental plant biology studies and in improving crop traits. These efforts often necessitate introduction and expression of multiple genes using promoters from a very limited repertoire. Current common practice of expressing multiple genes is the repeated use of the same or similar promoters. This practice causes more frequent transgene silencing due to a high degree of sequence homology and a greater chance of rearrangement among repeatedly used promoter sequences. Therefore, availability and use of natural bidirectional promoters to minimize gene silencing and achieve desirable expression pattern of transgenes is a critical issue in the field of plant genetic engineering. Here we describe the use of a single natural bidirectional promoter to drive the expression of two reporter genes in onion epidermal cells and in transgenic tobacco plants. We show that (1) the promoter drives the simultaneous expression of GUS and GFP reporter genes after transient expression and stable transformation, (2) the transcription is equally strong in both directions, (3) immediate upstream regions in each direction control transcription independently from each other, and (4) the reporter genes are expressed in leaves and stems but not in roots, as expected from the fact that the endogenous promoter controls the expression of two photosynthetic genes in Arabidopsis. Hence, use of bidirectional promoters in heterologous background provides a means to express multiple genes in transgenic plants and aids genetic engineering-based crop improvement.

BackgroundThe development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Using the tools of plant genetic engineering, a broad-spectrum antimicrobial gene was tested for resistance against head blight caused by Fusarium graminearum Schwabe, a devastating disease of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) that reduces both grain yield and quality.ResultsA construct containing a bovine lactoferrin cDNA was used to transform wheat using an Agrobacterium-mediated DNA transfer system to express this antimicrobial protein in transgenic wheat. Transformants were analyzed by Northern and Western blots to determine lactoferrin gene expression levels and were inoculated with the head blight disease fungus F. graminearum. Transgenic wheat showed a significant reduction of disease incidence caused by F. graminearum compared to control wheat plants. The level of resistance in the highly susceptible wheat cultivar Bobwhite was significantly higher in transgenic plants compared to control Bobwhite and two untransformed commercial wheat cultivars, susceptible Wheaton and tolerant ND 2710. Quantification of the expressed lactoferrin protein by ELISA in transgenic wheat indicated a positive correlation between the lactoferrin gene expression levels and the levels of disease resistance.ConclusionsIntrogression of the lactoferrin gene into elite commercial wheat, barley and other susceptible cereals may enhance resistance to F. graminearum.

Comamonas sp. strain CNB-1, isolated from activated sludge and having a strong ability to degrade 4-chloronitrobenzene (4CNB), was applied for rhizoremediation of 4CNB-polluted soil through association with alfalfa. Confocal laser scanning microscopy revealed that strain CNB-1 successfully colonized alfalfa roots. Determination of strain CNB-1 populations by cultivation method and by quantitative competitive PCR technique targeting the chloronitrobenzene nitroreductase gene showed that the population of strain CNB-1 in the rhizosphere was about 10-100 times higher than that in the bulk soil. Gnotobiotic and outdoor experiments showed that pollutant 4CNB was completely removed within 1 or 2 days after 4CNB application into soil, and that its phytotoxicity to alfalfa was eliminated by inoculation of strain CNB-1. Results from PCR-denaturing gradient gel electrophoresis and analysis of 16S rRNA gene libraries revealed that the indigenous soil microbial community mainly consisted of alphaproteobacteria, betaproteobacteria, gammaproteobacteria, the CFB bacteria (Cytophaga-Flavabacterium-Bacteriodes), and Acidobacteria. This microbial community was not significantly influenced by inoculation of strain CNB-1. Thus, this study has developed a Comamonas-alfalfa system for rhizoremediation of 4CNB.

The distribution of culturable bacteria in the rhizosphere, rhizoplane, and interior root tissues of moso bamboo plants was investigated in this study. Of the 182 isolates showing different colony characteristics on Luria-Bertani and King B plates, 56 operational taxonomic units of 22 genera were identified by 16S ribosomal RNA gene sequence analysis. The majority of root endophytic bacteria were Proteobacteria (67.5%), while the majority of rhizospheric and rhizoplane bacteria were Firmicutes (66.3% and 70.4%, respectively). The most common genus in both the rhizosphere and on the rhizoplane was Bacillus (42.4% and 44.4%, respectively), while Burkholderia was the most common genus inside the roots, comprising 35.0% of the isolates from this root domain. The endophytic bacterial community was less diverse than the rhizoplane and rhizospheric bacterial communities. Members of Lysinibacillus, Bacillus, and Burkholderia were found in all three root domains, whereas many isolates were found in only a single domain. Our results show that the population diversity of culturable bacteria is abundant in the root domains of moso bamboo plants and that obvious differences exist among the rhizospheric, rhizoplane, and endophytic bacterial communities.

A total of 985 bacterial strains with different colony characteristics were isolated from the root of tree peony plants (variety 'Fengdan' and 'Lan Furong'); 69 operational taxonomic units were identified by amplified ribosomal DNA restriction analysis. Representatives of each group were selected for partial 16S rRNA gene sequencing and phylogenetic analysis. The major groups in the bulk soil, rhizosphere, and rhizoplane of Fengdan were Firmicutes (63.2%), Actinobacteria (36.3%), and Betaproteobacteria (53.0%), respectively. The major bacteria groups in the bulk soil, rhizosphere, and rhizoplane of Lan Furong were Actinobacteria (34.8%), Gammaproteobacteria (45.2%), and Betaproteobacteria (49.1%), respectively. In total, the bacterial isolates comprised 26 genera--14 in the bulk soil, 14 in the rhizosphere, and 11 in the rhizoplane. The most common genus in the bulk soil of Fengdan and Lan Furong was Bacillus (49.6% and 32.6%, respectively), in the rhizosphere Microbacterium (21.1%) and Pseudomonas (42.0%), and in the rhizoplane Variovorax (53.0% and 49.1%, respectively). The results show that there are obvious differences in the bacterial communities in the three root domains of the two varieties, and the plants exerted selective pressures on their associated bacterial populations. The host genotypes also influenced the distribution pattern of the bacterial community.

Modal frequencies are widely used for vibration-based structural health monitoring (SHM) and for capturing the dynamics of a monitored structure to reveal possible failures. However, changing environmental and operational conditions (i.e., temperature, humidity, wind load, and traffic load) may submerge the modal variability induced by structural damage, thereby falsely identifying damage of interest. This paper presents a comprehensive summary review of SHM for the prediction of modal frequency and the elimination of environment-induced masking effects based on the data normalization method. The influence mechanisms of external variations on modal frequencies extensively reported in the literature are first described. Next, the research progress in predicting and eliminating the operational modal variability is reviewed emphatically; this progress can be primarily divided into an inputoutput method that focuses on the establishment of the relationship model between structural frequency and environmental conditions and an outputonly method that separates the embedded environmental variable-induced changes depending on whether the environmental measurements are measured. Finally, the conclusions and future studies are summarized and discussed. As an overview, the major contribution of this paper is to provide objective technical references for engineers and owners and to further evaluate structural safety conditions more effectively and in a timely manner.