Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings

Xiaojiao Liu,S Emilia Hannula,Xiaogang Li,Maria P.J Hundscheid,Paulien J.A Klein Gunnewiek,Anna Clocchiatti,Wei Ding,Wietse De Boer

doi:10.1016/j.soilbio.2021.108343

Xiaojiao Liu, S Emilia Hannula + Show 6 more

Open Access

https://doi.org/10.1016/j.soilbio.2021.108343

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Abstract

The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers.In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the assembly of root-associated bacteria and fungi of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet). Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. The soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia). Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. We show that cover crop elemental composition had a stronger effect than cover crop species identity. High quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. Tolerance of sugar beet seedlings against the fungal pathogen Rhizoctonia solani was correlated with residues causing increases of root-associated Oxalobacteraceae, Bacillaceae and Mortierellaceae. However, the same residues increased Fusarium-induced failure of asparagus seed germination. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.

Highlights

Root-associated micro-organisms live on the outside and inside of roots
Since the soil we used to grow the cash crops is naturally infested with pathogens for asparagus and sugar beet, we examined whether decomposing cover crop residues had an influ ence on the severity of damping-off diseases
Our results showed that decomposing cover crop residues have an impact on the assembly of microbial communities inhabiting cash crops roots

Summary

Introduction

Root-associated micro-organisms live on the outside (rhizoplane) and inside (endosphere) of roots. In these root habitats, microbiota perform various activities that have a strong impact on plant perfor mance. The impact of mutualistic and pathogenic microorganisms on plant perfor mance does depend on their presence in roots and on in teractions with each other and with other microbial root inhabitants (reviewed in (Sessitsch et al, 2019)). It is known that several microbial endophytes can have antagonistic activities against fungal pathogens via production of extracellular cell wall-degrading enzymes (i.e., chitinase and β-1,3-glucanase) and antimicrobial compounds (Compant et al, 2005; Carrion et al, 2019), induction of induced sys temic resistance (ISR) in host plants (Berendsen et al, 2018) and competition for space and resources (Philippot et al, 2013)

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