Title of the dataset:
Data and scripts from publication "Beetroot and Spinach Seed Microbiomes Can Suppress Pythium ultimum Infection; Results from a Large-Scale Screening"

Creators:
Makrina Diakaki
Liesbeth van der Heijden
Jorge Giovanny Lopez-Reyes 
Anita van Nieuwenhoven
Martje Notten
Mirjam Storcken
Patrick Butterbach

Contributors:
Joeke Postma
Wietse de Boer
Jürgen Köhl1


Related publication:
Diakaki et al. 2022

Description:
Seed health is an indispensable prerequisite of food security. While the toolkit of plant protection products is currently limited, evidence suggests that the seed microbiome could protect seeds from pathogens. Thus, given their possible disease suppressive potential, we tested 11 different pathosystems to achieve the following proof-of-concept: seed microbiomes are beneficial for seed health through conferring disease suppression. This study focused on beetroot, onion, spinach, pepper, coriander, red fescue and perennial ryegrass seeds, with each crop being challenged with one or two from a total of six pathogens, namely Pythium ultimum (or Pythium sp.), Setophoma terrestris, Fusarium oxysporum, Phytophthora capsici, Laetisaria fuciformis and Puccinia sp. Each seed lot of each crop was tested with and without treatment with a disinfectant as a proxy for comparing intact seed microbiomes with seed microbiomes after partial elimination by disinfection. We found disease suppression in two pathosystems. Beetroot and spinach seed lots were able to suppress disease caused by Pythium ultimum when their microbiomes were intact but not after seed disinfection. We speculate that this relates to the microorganisms residing on and in the seed. Yet, seed microbiome disease suppression was not found in all pathosystems, highlighting the variation in seed morphology, plant cultivars, pathogens and seed disinfection treatments. A holistic understanding of the characteristics of seeds that harbour suppressive microbiomes as well as the pathogens that are sensitive to suppression, could lead to more targeted and informed seed processing and treatment and, consequently, to the sustainable management of seedling diseases. 

Keywords:
Seed microbiome; disease suppression; seed disinfection; plant-pathogen bioassay


This dataset contains the following data files:

Beetroot_4Rgermination.csv
Beetroot4R_data.csv
Coriander_4Rgermination.csv
Coriander4R_data.csv
Onion_4Rgermination.csv
Onion4R_data.csv
OnionPhoma_4Rdata.csv
OnionPhoma_SpinachFusarium.csv
Pepper_4Rgermination.csv
Pepper_plant_4Rdata.csv
Pepper_seeds_4Rdata.csv
Perennial_puccinia_4Rdata.csv
Perennial_thread_4Rdata.csv
Red_fescue_4Rdata.csv
Spinach_4Rgermination.csv
Spinach4R_data.csv
SpinachFusarium_4Rdata.csv


Statistical analyses were run in R Studio. 
Scripts are included as:

01 data analysis.R
01b data dispersion.R
02 data analysis.R
03 data analysis and Fig.2.R
04 make Fig.1.R
05a make Fig.3.R
05b make Fig.3.R
06a make Suppl.Fig.1 continuous.R
06b make Suppl.Fig.1 ordinal.R
06c combine Suppl.Fig.1.R
summarySE_function.R


This dataset is published under the CC BY-NC-ND 4.0 (ttribution-NonCommercial-NoDerivatives 4.0 International) license.
