Eugene McAvoy

Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection

BackgroundEnriching environmental samples to increase the probability of detection has been standard practice throughout the history of microbiology. However, by its very nature, the process of enrichment creates a biased sample that may have unintended consequences for surveillance or resolving a pathogenic outbreak. With the advent of next-generation sequencing and metagenomic approaches, the possibility now exists to quantify enrichment bias at an unprecedented taxonomic breadth.FindingsWe investigated differences in taxonomic profiles of three enriched and unenriched tomato phyllosphere samples taken from three different tomato fields (n = 18). 16S rRNA gene meteganomes were created for each of the 18 samples using 454/Roche’s pyrosequencing platform, resulting in a total of 165,259 sequences. Significantly different taxonomic profiles and abundances at a number of taxonomic levels were observed between the two treatments. Although as many as 28 putative Salmonella sequences were detected in enriched samples, there was no significant difference in the abundance of Salmonella between enriched and unenriched treatments.ConclusionsOur results illustrate that the process of enriching greatly alters the taxonomic profile of an environmental sample beyond that of the target organism. We also found evidence suggesting that enrichment may not increase the probability of detecting a target. In conclusion, our results further emphasize the need to develop metagenomics as a validated culture independent method for pathogen detection.

Identification and isozyme characterisation of Meloidogyne spp. infecting horticultural and agronomic crops, and weed plants in Florida.

A total of 327 root samples collected from horticultural and agronomic crops, and weeds associated with these crops in Florida crop production regions, were examined. Isozyme phenotypes, esterase (EST) and malate dehydrogenase (MDH) phenotypes were used to characterise and identify the species of Meloidogyne present in these samples. At least 26 females from each sample were examined using polyacrylamide gel electrophoresis. Sixteen major bands of EST activity were found, corresponding to 12 phenotypes. A species-specific EST phenotype was consistently associated with each of the Meloidogyne spp. identified: Meloidogyne arenaria, M. floridensis, M. graminicola, M. hapla, M. incognita, M. javanica, M. mayaguensis and M. partityla. Two unique EST phenotypes, which have not been described, were found associated with three unidentified nematode populations. Five bands of MDH activity and four phenotypes were also found among the populations. During this study, new host records were determined for M. floridensis and M. mayaguensis, two recently reported Meloidogyne spp. in Florida. Plant species found as new hosts of M. floridensis were Cucumis sativus, Phaseolus sp., Solanum melongena and one weed species, Emilia sonchifolia, and the M. incognita-resistant peach rootstock ‘Flordaguard’. New hosts for M. mayaguensis were Carica papaya, Capsicum annuum var. Longum, and six weed plants, including Eclipta prostrata, Fatoua villosa, Panicum sp., Poinsettia cyathophora, Solanum americanum and also one unidentified weed species belonging to the family Acanthaceae. To our knowledge, Florida is the only geographic area of North America where M. floridensis and M. mayaguensis have been detected.

Effects of Water and Nutrient Strategies on Water Quality and Crop Yield

South Florida accounts for a large fraction of the vegetables produced in Florida. For a given crop season, the typical south Floridian vegetable grower applies fertilizer with a single application and irrigates via seepage irrigation. Large portions of fertilizer may leach to the ground water due to fluctuating high water table levels, which at times reach the soil surface. To account for leaching losses of fertilizer N, growers apply additional amounts of fertilizer to maximize yield. Environmental regulations such as TMDL require the implementation of water and nutrient BMPs to reduce the nutrient loadings to receiving water bodies. However, the effects of several BMPs on crop yield and water quality have not been quantified. A study was undertaken in south Florida to examine the effects of water and nutrient management practices on yield and water quality. Two vegetable production systems were installed and monitored simultaneously for two crop seasons. The first system involved the typical grower’s management practice in southwest Florida. The second system was similar to the grower’s management practice but soil moisture content was used to manage the water table and University of Florida fertilizer recommendations were used. Results revealed a significant difference in the crop yield between the two systems during the second crop season. This was likely due to leaching of relatively large amount of fertilizer N from the bed caused by a higher than normal rainfall. Surface and ground water quality data for the 2-year period are currently being compiled.