Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida

Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be “core” genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida

Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies

Current knowledge of plant virus diversity is biased towards agents of visible and economically important diseases. Less is known about viruses that have not caused major diseases in crops, or viruses from native vegetation, which are a reservoir of biodiversity that can contribute to viral emergence. Discovery of these plant viruses is hindered by the traditional approach of sampling individual symptomatic plants. Since many damaging plant viruses are transmitted by insect vectors, we have developed “vector-enabled metagenomics” (VEM) to investigate the diversity of plant viruses. VEM involves sampling of insect vectors (in this case, whiteflies) from plants, followed by purification of viral particles and metagenomic sequencing. The VEM approach exploits the natural ability of highly mobile adult whiteflies to integrate viruses from many plants over time and space, and leverages the capability of metagenomics for discovering novel viruses. This study utilized VEM to describe the DNA viral community from whiteflies (Bemisia tabaci) collected from two important agricultural regions in Florida, USA. VEM successfully characterized the active and abundant viruses that produce disease symptoms in crops, as well as the less abundant viruses infecting adjacent native vegetation. PCR assays designed from the metagenomic sequences enabled the complete sequencing of four novel begomovirus genome components, as well as the first discovery of plant virus satellites in North America. One of the novel begomoviruses was subsequently identified in symptomatic Chenopodium ambrosiodes from the same field site, validating VEM as an effective method for proactive monitoring of plant viruses without a priori knowledge of the pathogens. This study demonstrates the power of VEM for describing the circulating viral community in a given region, which will enhance our understanding of plant viral diversity, and facilitate emerging plant virus surveillance and management of viral diseases

An Economic Analysis of Fumigation Alternatives, the Methyl Bromide Ban, and its Implication: Evidence from the Florida Tomato Industry

Florida tomato industry is suffering from current methyl bromide phase-out under Montreal Protocol. Methyl bromide and its alternative fumigation strategies for producers are analyzed. This article seeks to provide growers and policy makers with scientific information on optimal fumigation strategies in terms of economic feasibility, financial efficiency and risk efficiency through partial budget analysis and stochastic efficiency with respect to a function

Design and Development of a Multi-Purpose Low-Cost Hyperspectral Imaging System

Hyperspectral image analysis is gaining momentum in a wealth of natural resources and agricultural applications facilitated by the increased availability of low-cost imaging systems. In this study, we demonstrate the development of the Vegetation Mobile Mapping System (VMMS), a low-cost hyperspectral sensing system that is supported by consumer-grade digital camera(s). The system was developed using off-the-shelf imaging and navigation components mainly for ground-based applications. The system integrates a variety of components including timing and positioning GPS receivers and an Inertial Measurement Unit (IMU). The system was designed to be modular and interoperable allowing the imaging components to be used with different navigation systems. The technique used for synchronizing captured images with GPS time was presented. A relative radiometric calibration technique utilizing images of homogeneous targets to normalize pixel gain and offset parameters was used. An empirical spectral calibration method was used to assign wavelengths to image bands. Data acquisition parameters to achieve appropriate spatial coverage were presented. The system was tested in ground-based data collection and analysis experiments that included water quality and vegetation studies

Perceptions of Polycom Programming for Delivery of Continuing Education to Florida\u27s Licensed Pesticide Applicators

Polycom technology has potential for efficient use of program delivery by Extension educators. A survey of licensed pesticide applicators attending a 1-day event at one of 20 host polycom sites revealed that polycom distance learning is effective for presenting information and learning. Responses also indicated that most of this audience is comfortable with the format of the polycom environment and would attend a similar type event in the future

Characterization of Verticillium dahliae and V. tricorpus isolates from lettuce and artichoke

Verticillium isolates collected from lettuce and artichoke were characterized for morphology, growth and pathogenicity. Several isolates were identified as Verticillium tricorpus based on morphological and cultural characteristics, including the production of dark resting mycelia, chlamydospores, microsclerotia, and yellow to orange pigmentation in culture. Compared with isolates of V dahliae, these isolates also produced microsclerotia and conidia that were significantly larger and exhibited a distinct growth pattern at varying temperatures. Using database sequence information, primers were developed from the internal transcribed spacer region to produce a diagnostic 337-bp product specific to V tricorpus and used to confirm the identification of isolates. Pathogenicity tests indicated that isolates of V tricorpus were weak pathogens, causing a median disease severity (DS) of 3.5 on lettuce and 5.0 on artichoke. Although lettuce and artichoke inoculated with isolates of V tricorpus exhibited reduced height and fresh foliar and root weight, the reductions were not statistically significant, unlike in plants inoculated with isolates of V dahliae. Lettuce co-inoculated with isolates of V tricorpus and V dahliae exhibited reduced symptoms of Verticillium wilt and improved growth relative to those inoculated with V dahliae alone. The early introduction of V tricorpus in soil-drench inoculations appeared to provide better relief from subsequent V dahliae inoculation than when the two species were co-inoculated simultaneously using the root-dip method, suggesting competitive exclusion as a plausible mechanism. A spore-polymerase chain reaction assay developed using cultured spores directly as template and primers specific to V tricorpus confirmed the presence of V tricorpus on inoculated roots. This work demonstrates the potential use of V tricorpus to directly reduce the effect of V dahliae on lettuce and artichoke and, to our knowledge, is the first reported characterization of V tricorpus isolates collected from lettuce and artichoke

Economics of fumigation in tomato production: the impact of methyl bromide phase-out on the Florida tomato industry

The Florida tomato industry is facing challenges of increased production costs and decreased yields resulting from the methyl bromide (MBr) phase-out under the Montreal Protocol for environmental concerns. MBr and several accepted alternative soil fumigant systems are analyzed in this study from an economic perspective. This article focuses on identifying optimal fumigant systems by analyzing the cost effectiveness and economic risk associated with MBr and several other commercially available soil fumigant systems using data collected from scientific field trials. The results obtained show that a 67:33 formulation of MBr: chloropicrin is the most cost-effective treatment, and no alternative fumigant systems investigated can substitute MBr cost-effectively in Florida tomato production. The analysis indicated that switching from MBr (67:33) to the new industry standard PicChlor 60 approximately resulted in a loss of $3,569 per acre in gross revenue and$1,656 per acre in profit using market prices in the 2013/14 season. Higher market prices would further increase the loss