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A symbiotic footprint in the plant root microbiome

Hartman, Kyle; Schmid, Marc W.; Bodenhausen, Natacha; Bender, S. Franz; Valzano-Held, Alain; Schlaeppi, Klaus and van der Heijden, Marcel (2023) A symbiotic footprint in the plant root microbiome. Environmental Microbiome, 18 (65), pp. 1-16.

[thumbnail of hartman-etal-2023-EnviromentalMicrobiome-Vol18_65-p1-16.pdf] PDF - English
Available under License Creative Commons Attribution.


Document available online at: https://link.springer.com/article/10.1186/s40793-023-00521-w


A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure.
We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts.
Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome – which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.

EPrint Type:Journal paper
Keywords:Arbuscular mycorrhizal fungi, Rhizobia, Symbiosis, Root microbiome, Plant species, Abacus, FiBL90525
Agrovoc keywords:
Subjects: Soil > Soil quality
Research affiliation: Switzerland > Agroscope
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Soil > Nutrient management
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Soil > Soil quality
Switzerland > University of Basel
Switzerland > University of Bern
Switzerland > Zürich University
Switzerland > Other organizations Switzerland
Related Links:https://www.fibl.org/en/themes/projectdatabase/projectitem/project/1937
Deposited By: Forschungsinstitut für biologischen Landbau, FiBL
ID Code:51778
Deposited On:09 Oct 2023 11:12
Last Modified:06 Dec 2023 09:18
Document Language:English
Refereed:Peer-reviewed and accepted

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