Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off

Makrina Diakaki; Beatriz Andreo Jimenez; Ezra de Lange; Patrick Butterbach; Liesbeth van der Heijden; Jürgen Köhl; Wietse de Boer; Joeke Postma

doi:10.1093/femsec/fiaf004

Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off

Makrina Diakaki^* (Corresponding author), Beatriz Andreo Jimenez, Ezra de Lange, Patrick Butterbach, Liesbeth van der Heijden, Jürgen Köhl, Wietse de Boer, Joeke Postma

^*Corresponding author for this work

NIOO - Microbial Ecology (ME)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

1 Citation (Scopus)

Abstract

Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

Original language	English
Article number	fiaf004
Journal	FEMS Microbiology Ecology
Volume	101
Issue number	2
DOIs	https://doi.org/10.1093/femsec/fiaf004
Publication status	Published - 08 Jan 2025

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10.1093/femsec/fiaf004Licence: CC BY-NC-ND

Cite this

@article{c6ff4934933f4d37a1372ddd654f0eba,

title = "Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off",

abstract = "Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.",

author = "Makrina Diakaki and Beatriz Andreo Jimenez and Ezra de Lange and Patrick Butterbach and Liesbeth van der Heijden and J{\"u}rgen K{\"o}hl and Wietse de Boer and Joeke Postma",

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doi = "10.1093/femsec/fiaf004",

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TY - JOUR

T1 - Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off

AU - Diakaki, Makrina

AU - Andreo Jimenez, Beatriz

AU - de Lange, Ezra

AU - Butterbach, Patrick

AU - van der Heijden, Liesbeth

AU - Köhl, Jürgen

AU - de Boer, Wietse

AU - Postma, Joeke

N1 - Data archiving: no NIOO data

PY - 2025/1/8

Y1 - 2025/1/8

N2 - Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

AB - Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

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