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Disease scores and microbial densities for seedlings in phage pre-treatment trials

Citation

Hernandez, Catherine (2020), Disease scores and microbial densities for seedlings in phage pre-treatment trials, Dryad, Dataset, https://doi.org/10.6078/D15T4M

Abstract

This dataset contains two files of results associated with a project testing phage pre-treatment of tomato seedlings prior to infection with Pseudomonas syringae pv. tomato strain DC3000. One file contains the disease scores of each seedling over time, and the other contains bacteria and phage densities at the endpoint of sampling. Bacterial densities were quantified using two methods (colony forming units and droplet digital PCR), and phage densities were quantified solely with droplet digital PCR.

Usage Notes

Disease scores file: This file contains the disease scores for inoculated seedlings in all three trials. Inoc_date is the inoculation date, Sample is the seedling/tube number within a given trial, Treatment is the inoculation treatment, Day is day post-inoculation, and Disease_score is the disease score on the specified day for each sample (following the scoring scheme of Morella et al. 2019). Treatment abbreviations are as follows: DC3000 only is “DC3000”,  DC3000 with phage FRS is “DC_FRS”, DC3000 with phage SHL is “DC_SHL”, DC3000 with autoclaved phage FRS is “DC_Autoclaved_FRS”, phage FRS only is “FRS”, phage SHL only is “SHL”, autoclaved phage FRS only is “AutoclavedFRS_ONLY”, and the magnesium chloride control is “MG_NEG”.

Densities file: This file contains the bacterial densities (in colony forming units and droplet digital PCR copies) and phage densities (in droplet digital PCR copies) adjusted for seedling weights in all trials. Inoc_date is the inoculation date, Sample is the seedling/tube number within a given trial, and Treatment is the inoculation treatment. Treatment abbreviations are as follows: DC3000 only is “DC3000”,  DC3000 with phage FRS is “DC_FRS”, DC3000 with phage SHL is “DC_SHL”, DC3000 with autoclaved phage FRS is “DC_Autoclaved_FRS”, phage FRS only is “FRS”, phage SHL only is “SHL”, autoclaved phage FRS only is “AutoclavedFRS_ONLY”, and the magnesium chloride control is “MG_NEG”. Colony forming unit (CFU) values are expressed per milliliter of seedling homogenate (“CFU_nonadjusted_permlhomog”), and per gram and milligram of seedling (“CFU_pergram” and “CFU_permg” respectively). ddPCR columns specify if they represent the value for bacteria (any column beginning with “ddPCR_B”) or phage P1 (any column beginning with “ddPCR_P”). ddPCR columns with “raw” at the end are copies per µL reaction from the droplet reader. ddPCR values with “adj_pergram” at the end have had the following calculation performed: raw values from reader x 10 (for sample dilution in water) x 10 (for dilution of sample in ddPCR reaction) x 1000 (to calculate copies per mL) * volume (in mL) seedling was homogenized in / weight of seedling in grams. “adj_permg” columns are the “adj_pergram” values divided by 1000. “rawpermg” columns are the copies per uL reaction from the droplet reader (“raw” columns), multiplied by the volume (in mL) the seedlings were homogenized in, divided by the seedling weight in milligrams.

 

In the June 25 trial (trial 1), two samples were removed due to caps falling off during seedling scoring.  Sample 13 was removed on the first day, and has no disease scores or densities associated with it. Sample 3 has disease scores for the first 3 days, but no further scores or densities.