Franklin Behlau

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

BackgroundBacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.ResultsWe sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.ConclusionsComparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.

Molecular Characterization of Copper Resistance Genes from Xanthomonas citri subsp. citri and Xanthomonas alfalfae subsp. citrumelonis

ABSTRACT Copper sprays have been widely used for control of endemic citrus canker caused by Xanthomonas citri subsp. citri in citrus-growing areas for more than 2 decades. Xanthomonas alfalfae subsp. citrumelonis populations were also exposed to frequent sprays of copper for several years as a protective measure against citrus bacterial spot (CBS) in Florida citrus nurseries. Long-term use of these bactericides has led to the development of copper-resistant (Cur) strains in both X. citri subsp. citri and X. alfalfae subsp. citrumelonis, resulting in a reduction of disease control. The objectives of this study were to characterize for the first time the genetics of copper resistance in X. citri subsp. citri and X. alfalfae subsp. citrumelonis and to compare these organisms to other Cur bacteria. Copper resistance determinants from X. citri subsp. citri strain A44(pXccCu2) from Argentina and X. alfalfae subsp. citrumelonis strain 1381(pXacCu2) from Florida were cloned and sequenced. Open reading frames (ORFs) related to the genes copL, copA, copB, copM, copG, copC, copD, and copF were identified in X. citri subsp. citri A44. The same ORFs, except copC and copD, were also present in X. alfalfae subsp. citrumelonis 1381. Transposon mutagenesis of the cloned copper resistance determinants in pXccCu2 revealed that copper resistance in X. citri subsp. citri strain A44 is mostly due to copL, copA, and copB, which are the genes in the cloned cluster with the highest nucleotide homology (≥92%) among different Cur bacteria.

Effect of Application Frequency and Reduced Rates of Acibenzolar-S-Methyl on the Field Efficacy of Induced Resistance Against Bacterial Spot on Tomato

Acibenzolar-S-methyl (ASM), a plant activator known to induce systemic acquired resistance, has demonstrated an ability to manage a number of plant diseases, including bacterial spot on tomato caused by four distinct Xanthomonas spp. The aim of this study was to evaluate application rate and frequency of ASM in order to optimize field efficacy against bacterial spot in Florida, while minimizing its impact on marketable yields. ASM was applied biweekly (once every 2 weeks) as a foliar spray at a constant concentration of 12.9, 64.5, and 129 μM throughout four field experiments during 2007-08. A standard copper program and an untreated control were also included. Overall, biweekly applications of ASM did not significantly reduce disease development or the final disease severity of bacterial spot compared with the copper-mancozeb standard or the untreated control. Only one experiment showed a significant reduction in the final disease severity on plants treated with ASM at 129 μM compared with the untreated control. Three additional field trials conducted during 2009-10 to evaluate the effects of weekly and biweekly applications of ASM at concentrations of 30.3 to 200 μM found that weekly applications provided significantly better disease control than biweekly applications. The tomato yields were not statistically improved with the use of ASM relative to the untreated control and standard copper program. Weekly ASM applications at rates as low as 75 μM (equivalent to 1.58 g a.i./ha in 100 liters of water or 0.21 oz. a.i./acre in 100 gallons of water) to 200 μM (equivalent to 4.20 g a.i./ha in 100 liters of water or 0.56 oz. a.i./acre in 100 gallons of water) were statistically equivalent in managing bacterial spot of tomato without significantly reducing yield compared with the untreated control.

Evidence for Acquisition of Copper Resistance Genes from Different Sources in Citrus-Associated Xanthomonads

ABSTRACT We determined that multiple and independent introductions of copper resistance genes have taken place for strains of Xanthomonas citri subsp. citri from Argentina and strains of X. alfalfae subsp. citrumelonis from Florida. This study compared the partial nucleotide sequences of principal copper resistance genes copL, copA, and copB from X. citri subsp. citri and X. alfalfae subsp. citrumelonis to strains of other Xanthomonas spp. resistant to copper that were isolated from 12 different countries or territories. The survey confirmed that the copLAB gene cluster is present in many species of Xanthomonas from different parts of the world. Alignment of partial nucleotide sequences of copper resistance genes among the copper-resistant (Cu(R)) strains of Xanthomonas detected homology of ≥92, ≥96, and ≥91% for copL, copA, and copB, respectively. Grouping of strains based on branching patterns of phylogenetic trees was similar for copL and copA but differed for copB. When the three genes were concatenated and analyzed using various phylogenetic methods, it appeared that the plasmid had been horizontally transferred and various populations were mutating based on selection pressure unique to geographic regions. Although high homology of the genes among the strains indicated that the copper resistance in xanthomonads has a common origin, the slight differences in nucleotide sequences within groups of strains indicated that Cu(R) genes have been independently exchanged among species of Xanthomonas throughout the world.

Monitoring for resistant populations of Xanthomonas citri subsp. citri and epiphytic bacteria on citrus trees treated with copper or streptomycin using a new semi-selective medium

Streptomycin has been tested as an alternative to copper bactericides, which are routinely used for the control of citrus canker (Xanthomonas citri subsp. citri, Xcc) in citrus producing areas where the disease is endemic. A major concern is that excessive use of copper as a bactericide may lead to development of copper-resistant strains of Xcc. In this study, we developed a semi-selective medium to recover copper or streptomycin-resistant strains of Xcc from citrus leaves. The newly developed semi-selective medium was used to monitor the effect of a 21-day-interval copper or streptomycin spray program on Xcc for three consecutive seasons and on citrus epiphytic bacterial populations for two seasons in a commercial grapefruit grove. Although, no copper- or streptomycin-resistant strains of Xcc were isolated after three seasons, we observed a significant increase over time in the frequency of citrus epiphytic bacteria resistant to these chemicals. Overall, the proportion of epiphytic bacteria resistant to streptomycin on treated and untreated leaves was proportionally lower than the copper-resistant bacterial population. When application of each bactericide was suspended for the season, the proportion of bactericide-resistant bacteria in the epiphytic population decreased to that of the non-treated bacterial population. Availability of an alternative bactericide, such as streptomycin, to integrate into a copper-based program would reduce the amount of each bactericide sprayed in citrus orchards and possibly lower the selection pressure for bacterial resistance to these chemicals.

Meio de cultura semi-seletivo para detecção de Curtobacterium flaccumfaciens pv. flaccumfaciens em solo e sementes de feijoeiro

Bacterial wilt, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is an important disease for bean (Phaseolus vulgaris L.) production in Southern Brazil. The use of contamined seeds is the major way to spread the bacterium. Although the occurrence of this disease in Brazil is recent, the seedborne bacterium hase been disseminated to most of the bean producing areas. The objective of this study was to adjust the CNS (Corynebacterium Nebraskense Selective Medium) to recover and detect the bacterium in infected soil as well as in bean seeds. Suspensions obtained from washing infected soil and bean seeds contamined by the bacterium were plated onto modified CNS medium. The modified CNS was efficient to recover the bacterium from both contaminated soil and bean seeds. The CNS established medium differed from the original by reducing the concentration of polymyxin B sulfate to 16 mg/l, excluding cyclohexamide and replacing Daconil 2787-F fungicide (530 mg/ml chlorothalonil) with Dacostar 500 (500 mg/ml chlorothalonil).

Critical Fungicide Spray Period for Citrus Black Spot Control in São Paulo State, Brazil

The period of citrus black spot (CBS) control used in South Africa (SA) and Australia, from October to January or February, has not been as effective in São Paulo (SP), Brazil. This study aimed to evaluate different periods of protection and determine the critical period for CBS control in SP. A field trial was carried out for two seasons in a mature Valencia sweet orange orchard located in Mogi Guaçu, SP. Spray programs with a total of 60, 100, 140, 180, and 220 days of fruit protection (DFP) were evaluated. CBS symptoms and fruit drop decreased exponentially as the length of the period of protection increased. The reductions in CBS intensity and crop loss with these programs ranged from 34 to 96 and 50 to 77%, respectively. The programs with 180 and 220 DFP, which protected the fruit from September to March and May, showed the highest cost benefit. The critical period needed for CBS control in SP is longer than that in SA and Australia. The results obtained with the present study are helpful for scheduling a more efficient and rational program for CBS control not only in SP but also in other tropical and subtropical regions with similar weather conditions.

Thirteen decades of antimicrobial copper compounds applied in agriculture. A review

Since the initial use of Bordeaux mixture in 1885 for plant disease control, a large number of copper-based antimicrobial compounds (CBACs) have been developed and applied for crop protection. While these compounds have revolutionized crop protection in the twentieth century, their continuous and frequent use has also raised concerns about the long-term sustainability of copper (Cu)-based crop protection system. Here, we review CBACs used in crop protection and highlight their benefits and risks, and potential for their improvement and opportunities for further research to develop alternatives to CBACs. The major findings are (i) the relatively high toxicity to plant pathogens, low cost, low mammalian toxicity of the fixed Cu compounds, and their chemical stability and prolonged residual effects are major benefits of these compounds; (ii) phytotoxicity, development of copper-resistant strains, soil accumulation, and negative effects on soil biota as well as on food quality parameters are key disadvantages of CBACs; (iii) regulatory pressure in agriculture worldwide to limit the use of CBACs has led to several restrictions, including that imposed by the regulation 473/2002 in the European Union; and (iv) mitigation strategies to limit the negative effects of CBACs include their optimized use, soil remediation, and development and application of alternatives to CBACs for a sustainable crop protection. We conclude that recent research and policy efforts have led to the development of a number of alternatives to CBACs, which should be further intensified to ensure that growers have sufficient tools for the implementation of sustainable crop protection strategies.