Zhouqi Cui

In vitro Biofumigation of Brassica Tissues Against Potato Stem Rot Caused by Sclerotinia sclerotiorum

State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China (Received on November 30, 2011; Revised on May 2, 2012; Accepted on May 14, 2012)Sclerotinia sclerotiorum is a serious pathogen whichcauses yield loss in many dicotyledonous crops includ-ing potato. The objective of this study was to assess thepotential of biofumigation using three Brassica cropsincluding Brassica napus, B. juncea and B. campestrisagainst potato stem rot caused by S. sclerotiorum by invitro tests. Both macerated and irradiated dried tissueswere able to reduce radial growth and sclerotiaformation of five pathogen isolates on PDA, but mace-rated live tissues were more effective. Compared withother tested crops, B. juncea showed more inhibitoryeffect against the pathogen. The volatile compoundsproduced from macerated tissues were identified usinga gas chromatograph-mass spectrometer. The mainidentified compounds were methyl, allyl and butyl iso-thiocyanates. Different concentrations of these com-pounds inhibited mycelial growth of the pathogen invitro when applied as the vapor of pure chemicals. Anegative relationship was observed between chemicalsconcentrations and growth inhibition percentage. In thisstudy, it became clear that the tissues of local Brassicacrops release glucosinolates and have a good potential tobe used against the pathogen in field examinations. Keywords : dual culture, glucosinolates, ion trap detector,volatile compoundsPotato white mold, also known as stem rot, is a damagingdisease caused by the fungus Sclerotinia sclerotiorum. Thisdisease usually occurs in a large number of potato fieldsin Hamadan, Iran (Ojaghian, 2009) resulting in reducedyield and tuber quality. Application of fungicides, mainlyiprodione and dichloran, is the only control method beingused by local growers and it has caused environmentalconcerns leading to find non-chemical control methods suchas biofumigation.It has been shown in numerous studies that the use ofBrassica crops as green manure provides promising alter-natives to synthetic chemical fumigants (Brown and Morra,1997). Brassica crops are considered as break crops becausethey are able to break the life cycle of several soil bornepathogens such as wheat take-all (Brennan and Murray,1988). They have been proved to be effective againstnumerous nematodes (Buskov et al., 2002), fungal plantpathogens (Kirkegaard et al., 1996) and weeds (Boydston andHang, 1995). These biocontrolling effects are attributed to theproduction of volatile biotoxic compounds through a processwhich is known as biofumigation. The cruciferous tissuespossess thioglucoside compounds known as glucosinolates(GSLs), the secondary polar sulfur metabolites, which are thereason for the sharp or biting taste of condiments or theflavors of different edible Brassica tissues (McGregor et al.,1983). The GSLs are not harmful to organisms by themselvesbut they can change into isothiocyanates (ITCs), nitriles,thiocyanates, and oxazolidinethiones and other toxic com-pounds (Bending and Lincoln, 1999) by the endogenousenzyme myrosinase when Brassica tissues are damaged(Bones and Rossiter, 1996). The quality of the hydrolysisproducts depends on the type of organic side chain on theparent molecule and the environmental conditions (Rosa etal., 1997). No research has been conducted on the presence andidentification of GSLs in Iranian cultivars of Brassicas. Theobjective of this study was to evaluate the potential of bio-fumigation using three local Brassica crops against a numberof S. sclerotiorum isolates by in vitro experiments.Firstly, the inhibitory effects of Brassica tissues on radialgrowth and sclerotia formation of S. sclerotiorum weredetermined. Five highly aggressive isolates of S. sclerotiorum(Sc18d; Bahar, Sd6b; Bahar, Sd21n; Lalehjin, Sc59k; Baharand Sa21b; Lalehjin) were obtained from the CultureCollection of Plant Pathology Laboratory, Agriculture College,BuAli Sina University, Hamadan, Iran. These isolates hadalready been sampled in five heavily infected potato fields inHamadan province. The isolates were routinely cultured onpotato dextrose agar (PDA, 39 g/L; Merck, Darmstadt,Germany) and stored at 4 ± 1

Transcriptome analysis of Acidovorax avenae subsp. avenae cultivated in vivo and co-culture with Burkholderia seminalis

Response of bacterial pathogen to environmental bacteria and its host is critical for understanding of microbial adaption and pathogenesis. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. Results revealed a slight response to other bacteria, but a strong response to host. In particular, a large number of virulence associated genes encoding Type I to VI secretion systems, 118 putative non-coding RNAs, and 7 genomic islands (GIs) were differentially expressed in vivo based on comparative genomic and transcriptomic analyses. Furthermore, the loss of virulence for knockout mutants of 11 differentially expressed T6SS genes emphasized the importance of these genes in bacterial pathogenicity. In addition, the reliability of expression data obtained by RNA-Seq was supported by quantitative real-time PCR of the 25 selected T6SS genes. Overall, this study highlighted the role of differentially expressed genes in elucidating bacterial pathogenesis based on combined analysis of RNA-Seq data and knockout of T6SS genes.

Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818

Pseudomonas fuscovaginae is a phytopathogenic bacterium causing bacterial sheath brown rot of cereal crops. Here, we present the draft genome sequence of P. fuscovaginae CB98818, originally isolated from a diseased rice plant in China. The draft genome will aid in epidemiological studies, comparative genomics, and quarantine of this broad-host-range pathogen.

Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria

Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.

Gene Expression of Type VI Secretion System Associated with Environmental Survival in Acidovorax avenae subsp. avenae by Principle Component Analysis

Valine glycine repeat G (VgrG) proteins are regarded as one of two effectors of Type VI secretion system (T6SS) which is a complex multi-component secretion system. In this study, potential biological roles of T6SS structural and VgrG genes in a rice bacterial pathogen, Acidovorax avenae subsp. avenae (Aaa) RS-1, were evaluated under seven stress conditions using principle component analysis of gene expression. The results showed that growth of the pathogen was reduced by H2O2 and paraquat-induced oxidative stress, high salt, low temperature, and vgrG mutation, compared to the control. However, pathogen growth was unaffected by co-culture with a rice rhizobacterium Burkholderia seminalis R456. In addition, expression of 14 T6SS structural and eight vgrG genes was significantly changed under seven conditions. Among different stress conditions, high salt, and low temperature showed a higher effect on the expression of T6SS gene compared with host infection and other environmental conditions. As a first report, this study revealed an association of T6SS gene expression of the pathogen with the host infection, gene mutation, and some common environmental stresses. The results of this research can increase understanding of the biological function of T6SS in this economically-important pathogen of rice.

Susceptibility of Opportunistic Burkholderia glumae to Copper Surfaces Following Wet or Dry Surface Contact

Burkholderia glumae has been proposed to have a potential risk to vulnerable communities. In this work, we investigated the antibacterial activity and mechanism of copper surfaces against multi-drug resistant B. glumae from both patients and rice plants. The susceptibility of B. glumae to copper surfaces was noted by a significant decline in viable bacterial counts, relative to the slight reduction of stainless steel and polyvinylchloride, both of which were used as control surfaces. The mode of action of bacterial killing was determined by examing the mutagenicity, DNA damage, copper ions accumulation, and membrane damage in bacterial cells. The results indicated that the cells exposed to copper surfaces did not cause severe DNA lesions or increase the mutation frequencies, but resulted in a loss of cell membrane integrity within minutes. Furthermore, bacterial cells exposed to copper surfaces accumulated significantly higher amounts of copper compared to control surfaces. Overall, this study showed that metallic copper had strong antibacterial effect against B. glumae by causing DNA and membrane damage, cellular accumulation of copper, and cell death following DNA degradation, which could be utilized to reduce the risk of bacterial contamination and infection.

Genome Sequence of the Plant Pathogen Pseudomonas syringae pv. panici LMG 2367

Pseudomonas syringae pv. panici is a phytopathogenic bacterium causing brown stripe disease in economically important crops worldwide. Here, we announce the draft genome sequence of Pseudomonas syringae pv. panici LMG2367 to provide further valuable insights for comparison of the pathovars among species Pseudomonas syringae.