Development and survival of axenic onion fly (Delia antiqua (Meigen)) larvae reared on axenic onions were similar to that of larvae reared in the presence of naturally associated microorganisms. The only consistent difference was a 20–50% increase in the duration of the larval stage for axenic larvae. Contrary to current opinions, onion fly larvae can function as true herbivores on onions. RÉSUMÉ La mouche de l'oignon, Delia antiqua: sa survie et son développement sur oignons en présence ou en absence de microorganismes Le besoin en microorganismes dans les relations entre Delia antiqua (Meigen) et l'oignon est admis depuis plusieurs décennies. Nous avons constaté que le développement et la survie de larves axéniques élevées sur oignon sont semblables à ceux des larves élevées en présence des microbes normalement associés aux oignons ou aux larves. La principale différence entre les conditions axéniques ou non a été une prolongation de 20 à 50% développement larvaire en conditions axéniques. Bien que cette différence puisse ětre écologiquement importante, nous suggérons que les microorganismes peuvent ětre intéressants pour des raisons autres que nutritives si ces relations entre insectes et microbes ne sont pas fortuites. En clair, les larves de mouches de l'oignon peuvent agir comme de véritables herbivores sur l'oignon.

The Centers for Disease Control and Prevention recently emphasized the need for enhanced technologies to use in investigations of outbreaks of foodborne illnesses. To address this need, e-probe diagnostic nucleic acid analysis (EDNA) was adapted and validated as a tool for the rapid, effective identification and characterization of multiple pathogens in a food matrix. In EDNA, unassembled next generation sequencing data sets from food sample metagenomes are queried using pathogen-specific sequences known as electronic probes (e-probes). In this study, the query of mock sequence databases demonstrated the potential of EDNA for the detection of foodborne pathogens. The method was then validated using next generation sequencing data sets created by sequencing the metagenome of alfalfa sprouts inoculated with Escherichia coli O157:H7. Nonspecific hits in the negative control sample indicated the need for additional filtration of the e-probes to enhance specificity. There was no significant difference in the ability of an e-probe to detect the target pathogen based upon the length of the probe set oligonucleotides. The results from the queries of the sample database using E. coli e-probe sets were significantly different from those obtained using random decoy probe sets and exhibited 100% precision. The results support the use of EDNA as a rapid response methodology in foodborne outbreaks and investigations for establishing comprehensive microbial profiles of complex food samples.

The advancement in high-throughput sequencing (HTS) technology allows the detection of pathogens without the need for isolation or template amplification. Plant regulatory agencies worldwide are adopting HTS as a pre-screening tool for plant pathogens in imported plant germplasm. The technique is a multipronged process, and often the bioinformatic analysis complicates detection. Previously we developed E-probe Diagnostic Nucleic acid Analysis (EDNA), a bioinformatic tool that detects pathogens in HTS data. EDNA uses custom databases of signature nucleic acid sequences (e-probes) to reduce computational effort and subjectivity when determining pathogen presence in a sample. E-probes of Pythium ultimum (Trow) and Phytophthora ramorum (Werres, De Cock & Man in’t Veld) were previously validated only using simulated HTS data. However, HTS samples generated from infected hosts or pure culture may vary in pathogen concentration, sequencing bias, and data quality, suggesting that each pathosystem requires further validation. Here we used metagenomic and genomic HTS data generated from infected hosts and pure culture respectively, to further validate and curate e-probes of Py. ultimum and Ph. ramorum. E-probe length was found to be a determinant of diagnostic sensitivity and specificity; 80-nucleotides e-probes increased the diagnostic specificity to 100%. Curating e-probes to increase specificity affected diagnostic sensitivity only for 80-nucleotides Py. ultimum e-probes. Comparing e-probes with alternative databases and bioinformatic tools in their speed and ability to find Py. ultimum and Ph. ramorum demonstrated that while pathogen sequence reads were detected by other methods, they were less specific and slower when compared with e-probes.

When given a choice of feeding sites in laboratory arenas, Delia antiqua (Meigen) larvae exhibited a 3:1 bias for internal vs outer sections of onion bulbs and distributed themselves non‐randomly among identical preferred onion sections. Larval clustering did not appear to be correlated with increased fitness in the laboratory; larval development was identical across the range of densities from 1 to 50 larvae per onion. Larvae feeding on preferred internal sections developed 14% faster, were 38% heavier upon pupation, and were two times more likely to survive to the adult stage than larvae feeding on outer sections. D. antiqua larval food preference was therefore positively correlated with increased fitness.