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Beetroot and spinach seed microbiomes can suppress Pythium ultimum infection: results from a large-scale screening

Published online by Cambridge University Press:  07 September 2022

Makrina Diakaki*
Affiliation:
Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands Soil Biology Group, Wageningen University and Research, Wageningen, the Netherlands
Liesbeth van der Heijden
Affiliation:
Bejo Zaden B.V., Warmenhuizen, the Netherlands
Jorge Giovanny Lopez-Reyes
Affiliation:
DLF B.V., Kapelle, the Netherlands
Anita van Nieuwenhoven
Affiliation:
Pop Vriend Seeds B.V., Andijk, the Netherlands
Martje Notten
Affiliation:
Nunhems Netherlands B.V. (BASF), Nunhem, the Netherlands
Mirjam Storcken
Affiliation:
CN Seeds Ltd., Ely, UK
Patrick Butterbach
Affiliation:
Germains Seed Technology, Enkhuizen, the Netherlands
Jürgen Köhl
Affiliation:
Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
Wietse de Boer
Affiliation:
Soil Biology Group, Wageningen University and Research, Wageningen, the Netherlands Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
Joeke Postma
Affiliation:
Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
*
*Correspondence: Makrina Diakaki, E-mail: makrina.diakaki@wur.nl
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Abstract

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 can be 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 a Pythium sp.), Setophoma terrestris, Fusarium oxysporum, Phytophthora capsici, Laetisaria fuciformis and a mix of Puccinia sp. isolates. 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 P. 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.

Information

Type
Research Paper
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press
Figure 0

Table 1. Crops, seed disinfection treatments and pathogens used to assess the potential effects of the seed microbiome on disease suppressiona

Figure 1

Table 2. Selected disease variables and data types in the different bioassays used to assess the potential effects of the seed microbiome on disease suppression

Figure 2

Table 3. Definition of seed lot categories based on susceptibility of disinfected seeds compared to non-treated seeds in a bioassay to assess the potential effects of seed microbiomes on disease suppression

Figure 3

Fig. 1. Total number of seed lots per crop for which seed germination was not affected by the seed disinfection treatment (generalized linear model, α = 0.05; with one exception: pepper germination cut-off threshold of 3% difference). The size of each circle is proportional to the number of seed lots.

Figure 4

Fig. 2. Total number of seed lots per bioassay considered positively responsive (blue), non-responsive (yellow) or negatively responsive (red) based on the outcome of each bioassay per seed lot (generalized linear model, α = 0.05 and false discovery rate correction α = 0.10 for all bioassays; exceptions: proportional odds logistic model, α = 0.05 for pepper plants – P. capsici bioassay; onion – S. terrestris and spinach – F. oxysporum f. sp. spinaciae bioassays cut-off threshold of 2 in 10 or 1 in 5 scale index levels). Specifications for each disease variable can be found in Table 2. The size of each circle is proportional to the number of seed lots.

Figure 5

Fig. 3. Seed lot performance per bioassay per disease variable (generalized linear model, α = 0.05 and false discovery rate correction α = 0.10 for all bioassays; exceptions: proportional odds logistic model, α = 0.05 for pepper plants – P. capsici bioassay; onion – S. terrestris and spinach – F. oxysporum f. sp. spinaciae bioassays cut-off threshold of 2 in 10 or 1 in 5 scale index levels). The performance of non-treated and disinfected seeds is plotted on the x and y axis, respectively. Each data point represents the mean (count data) or median (ordinal data) value of an individual seed lot. Data points are colour-coded according to category. Higher levels signify increased infection/presence of symptoms in all graphs. Days post-inoculation is abbreviated as ‘dpo’ and damping-off is abbreviated as d.o.

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